UPPSALA UNIVERSITY

Validation of CA-only models

This page contains some supplementary material to: G J Kleywegt, "Validation of protein models from CA coordinates alone", Journal of Molecular Biology, 273, 371-376 (1997).

Analysis of the distributions of CA-CA distances and of CA backbone angles and dihedrals for 88 CA-only models from the PDB. If an entry differs by more than 3 e.s.d.'s from the mean, the number of e.s.d.'s it lies removed from the mean is shown in parentheses. Three structures that are known to be wrong have been added for comparison: the intentionally backwards-traced models of CRABP II and A2U, and the original model of NQase. Other models in this list which are known to be wrong include 1PHY and 1PTE. Model 1SRX was handbuilt and the coordinates were derived from that with a precision of 0.1 Å.

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I - Typical values for 1343 X-ray structures determined at 2.0 Å resolution or better

Poor CA-CA distances (%) Trans CA-CA distances (%) Long CA-CA distances (%) Core angle/dihedral regions (%) Disallowed angle/dihedral regions (%)
1.5 (3.5) 96.8 (7.0) 1.4 (4.0) 72.8 (8.9) 3.1 (2.2)


II - Values for three known wrong models

PDB code Resolution (Å) Poor CA-CA distances (%) Trans CA-CA distances (%) Long CA-CA distances (%) Core angle / dihedral regions (%) Disallowed angle / dihedral regions (%)
CRABP (traced backwards on purpose and subsequently refined) 3.0 0.0 98.5 1.5 40.5 (3.6) 15.9 (5.8)
A2U (traced backwards on purpose and subsequently refined) 3.0 3.9 94.9 1.3 52.5 14.7 (5.3)
NQase (original model of asparaginase/glutaminase; coordinates courtesy of Dr. A. Wlodawer) 2.8 10.7 84.8 4.6 22.9 (5.6) 29.7 (12.1)


III - Values for 88 CA-only models in the PDB

PDB code Resolution (Å) Year Poor CA-CA distances (%) Trans CA-CA distances (%) Long CA-CA distances (%) Core angle / dihedral regions (%) Disallowed angle / dihedral regions (%)
1ENG 1.6 1993 0.0 100.0 0.0 59.2 5.0
1ABH 1.7 1992 0.0 100.0 0.0 75.6 2.1
2MBP 1.7 1992 0.8 95.4 3.8 79.0 2.4
1C53 1.8 1991 0.0 100.0 0.0 78.5 3.1
1LVD 1.8 1994 8.7 88.4 2.9 65.9 4.4
1MAR 1.8 1993 0.0 100.0 0.0 75.0 1.4
1TGL 1.9 1990 6.8 72.6 (3.4) 20.2 (4.7) 70.1 4.5
1ILT 2.0 1994 0.0 99.3 0.0 67.1 6.5
1TIA 2.0 1993 0.7 91.8 6.7 69.8 6.9
2BLM 2.0 1990 1.6 94.8 3.5 72.4 3.5
3CBH 2.0 1990 0.3 98.4 0.8 70.3 3.6
1TCT 2.1 1995 0.5 93.9 5.6 85.5 0.6
1RMI 2.15 1994 0.0 100.0 0.0 89.0 0.7
1BGT 2.2 1994 0.0 100.0 0.0 76.6 2.3
1BGU 2.2 1994 0.0 100.0 0.0 77.0 0.7
1CRO 2.2 1987 2.3 91.9 4.6 75.3 3.8
1PCL 2.2 1993 0.0 99.7 0.0 60.4 6.0
1NRD 2.3 1991 23.2 (6.2) 70.2 (3.8) 6.0 53.9 8.8
1XIA 2.3 1988 0.1 95.2 4.5 73.4 3.3
2ILA 2.3 1991 4.2 91.6 4.2 66.9 9.8 (3.0)
2RIG 2.3 1993 0.0 99.2 0.9 63.7 6.2
3HTC 2.3 1993 1.8 96.1 2.1 62.5 6.0
1ABN 2.4 1992 18.1 (4.7) 72.2 (3.5) 9.7 (2.1) 69.9 1.4
1PHY 2.4 1989 25.0 (6.7) 57.3 (5.6) 17.7 (4.1) 25.7 (5.3) 26.6 (10.7)
1ALR 2.48 1994 1.3 97.7 1.0 70.6 5.2
1AGS 2.5 1995 0.5 99.1 0.5 78.2 2.4
1AIN 2.5 1992 0.6 96.8 2.6 83.4 1.4
1CBP 2.5 1988 0.0 100.0 0.0 59.5 4.1
1GSB 2.5 1993 0.0 98.6 0.0 76.9 4.0
1GSC 2.5 1993 0.0 98.6 0.0 77.2 4.0
1HMC 2.5 1993 1.7 96.2 2.1 79.3 1.4
1HBP 2.5 1993 3.8 94.9 1.3 71.3 2.8
1MLE 2.5 1990 13.5 (3.4) 79.0 7.5 69.8 4.0
1TRT 2.5 1994 1.0 91.8 7.2 82.7 1.1
1UDP 2.5 1992 19.5 (5.1) 76.8 3.6 73.1 4.8
1XYS 2.5 1994 0.3 99.7 0.0 71.2 3.5
3DPA 2.5 1991 5.1 91.7 3.2 65.4 5.0
1IFA 2.6 1991 1.3 96.8 1.9 66.7 7.2
1POS 2.6 1993 0.0 100.0 0.0 63.2 3.1
1PYK 2.6 1980 19.2 (5.1) 32.0 (9.2) 47.7 (11.6) 42.7 (3.4) 15.4 (5.6)
1TIC 2.6 1993 3.6 88.9 6.6 67.4 6.8
1XAS 2.6 1994 1.0 97.3 1.7 73.1 3.0
2TLD 2.6 1991 8.1 84.7 6.9 57.2 6.5
1EFG 2.7 1994 0.2 99.2 0.6 61.6 5.8
1EFM 2.7 1987 21.2 (5.6) 74.4 (3.2) 4.5 55.7 13.6 (4.8)
1REA 2.7 1991 0.3 98.3 1.0 77.1 2.6
2CHY 2.7 1990 21.4 (5.7) 57.1 (5.6) 20.6 (4.8) 71.6 7.8
1AAT 2.8 1982 58.2 (16.2) 19.4 (11.0) 22.4 (5.2) 37.6 (4.0) 23.4 (9.2)
1ASI 2.8 1994 0.0 100.0 0.0 69.4 4.1
1BN2 2.8 1990 3.5 92.2 4.4 55.7 10.4 (3.3)
1CPB 2.8 1976 12.5 (3.1) 79.4 7.5 57.0 9.7 (3.0)
1DPI 2.8 1987 0.4 99.3 0.4 61.5 8.2
1GSG 2.8 1990 0.6 98.9 0.6 73.9 3.3
1LZ2 2.8 1981 4.7 91.3 1.6 47.3 7.1
1MYS 2.8 1993 9.2 90.3 0.5 74.8 2.9
1NRC 2.8 1992 1.9 98.1 0.0 70.0 6.7
1PTE 2.8 1985 11.3 68.6 (4.0) 20.1 (4.7) 28.7 (5.0) 33.0 (13.6)
1RDH 2.8 1993 0.0 99.6 0.4 74.0 3.6
1SRX 2.8 1976 17.9 (4.7) 41.5 (7.9) 37.7 (9.1) 35.4 (4.2) 18.8 (7.1)
1TPT 2.8 1990 0.2 99.8 0.0 74.4 2.5
1DEG 2.9 1993 7.8 61.0 (5.1) 31.2 (7.4) 53.1 4.7
1PEL 2.95 1993 6.1 85.7 7.9 57.3 10.6 (3.4)
1DLA 3.0 1993 0.7 93.8 5.4 73.8 1.2
1EPS 3.0 1991 8.2 86.4 5.4 72.3 4.2
1HMI 3.0 1993 19.8 (5.2) 68.7 (4.0) 11.5 57.7 10.0 (3.1)
1KAN 3.0 1993 10.5 89.1 0.4 73.7 3.2
1PHS 3.0 1990 5.0 87.0 8.0 65.9 4.5
2AT2 3.0 1992 5.9 83.7 10.4 54.7 9.6 (3.0)
2HVP 3.0 1989 0.0 100.0 0.0 48.1 18.2 (6.9)
5TGL 3.0 1991 2.3 89.8 6.4 69.4 4.1
1LRP 3.2 1987 1.2 94.3 4.6 63.3 7.6
1THI 3.2 1989 27.8 (7.5) 53.7 (6.1) 17.1 (3.9) 35.2 (4.2) 22.9 (9.0)
2IRT 3.2 1994 0.0 98.3 1.7 53.6 9.4
1MLI 3.3 1989 14.9 (3.8) 74.5 (3.2) 10.6 55.1 13.5 (4.7)
2RNP 3.3 1993 32.0 (8.7) 48.9 (6.8) 19.1 (4.4) 33.2 (4.4) 25.0 (9.9)
1GDR 3.5 1993 3.0 97.0 0.0 69.8 4.7
1HIG 3.5 1991 4.5 85.4 10.1 72.8 3.2
1HLA 3.5 1987 48.1 (13.3) 31.9 (9.2) 18.4 (4.2) 47.6 17.5 (6.5)
1KGA 3.5 1978 8.8 25.7 (10.1) 64.3 (15.7) 41.4 (3.5) 21.9 (8.5)
1PGI 3.5 1977 0.4 98.4 1.2 46.5 (3.0) 19.8 (7.6)
4CRO 3.9 1990 2.7 89.4 7.1 67.3 9.9 (3.1)
1HR3 5.5 1983 0.0 98.3 0.0 81.7 0.9
1HRB 5.5 1976 0.9 98.2 0.0 78.9 5.8
1LZH 6.0 1981 0.0 100.0 0.0 67.8 3.5
1PPS 6.0 1993 0.2 98.5 1.3 96.4 1.0
2LZH 6.0 1981 0.0 100.0 0.0 67.3 3.5
5PFK 7.0 1988 4.1 95.6 0.3 78.1 2.2
2TMA 15.0 1987 1.2 95.2 3.5 96.9 0.9


IV - Observed distribution of CA-CA distances (for 1,343 protein structures determined at 2.0 Å or better)

Class Distance range (Å) Population (%) E.s.d. (%) Observed range (%)
Short < 2.8 0.008 0.08 0.0 - 1.9
Cis 2.8 - 3.0 0.2 0.5 0.0 - 3.5
Poor 3.0 - 3.7 1.5 3.5 0.0 - 29.5
Trans 3.7 - 3.9 96.8 7.0 37.5 - 100.0
Long > 3.9 1.4 4.0 0.0 - 39.3


V - Definition and observed distribution of CA-backbone angles and dihedrals (for 1,343 protein structures determined at 2.0 Å or better). (Squares are 3 degrees by 3 degrees.)

Region Residues per square Area of plot (%) Population (%) E.s.d. (%)
Core > 99 7.1 72.8 8.9
Additional allowed 50 - 99 5.2 12.8 4.0
Generously allowed 10 - 50 15.0 11.3 4.6
Disallowed < 10 72.6 3.1 2.2

Latest update at 29 August, 2001.