. 2011 Aug 17;101(4):899–909. doi: 10.1016/j.bpj.2011.06.063

Table 1.

TOP structure refinement

Protein		APC22750
		Initial	TOP^∗		Initial	TOP^∗
		Initial	Stage 1	Stage 2	Initial	Stage 1	Stage 2
Resolution		2.09–25.0 Å			2.09–25.0 Å
Number of residues		465			480
Starting model		During refinement			Deposited (1VR4)
C_α-RMSD (Å)		N/A	0.71	0.42	N/A	0.46	0.14
<TSP>		3.31	−0.4	0.08	0.45	−1.2	−0.9
No. of H-bonds^†		162	190	214	239	249	263
R-work		0.3091	0.3880	0.2979 (0.2983)^‡	0.2061	0.3150	0.2087 (0.2074)^‡
R-free		0.3537	0.4233	0.3163 (0.3403)	0.2647	0.3507	0.2372 (0.2589)
Map correlation		0.76	0.66	0.77	0.85	0.76	0.85
RMSD from ideal	Bond length (Å)	0.045	0.047	0.040	0.014	0.017	0.016
RMSD from ideal	Angle (°)	2.567	2.904	3.130	1.692	1.935	1.810
RamaMap statistics (%)
Preferred^§		79	88	88	92	92	93
Allowed		6	3	4	5	5	4
Outliers		15	9	8	3	3	3

Protein		Cytochrome b₆f complex			A-Cobratoxin-ACHBP complex
		Initial	TOP^∗		Initial	TOP^∗
		Initial	Stage 1	Stage 2	Initial	Stage 1	Stage 2
Resolution		3.00–39.30 Å			4.20–25.0 Å
No. of residues		959			1356
Starting model		Deposited (2E74)			Deposited (1YI5)
C_α-RMSD (Å)		N/A	0.78	0.40	N/A	0.8	0.62
<TSP>		2.92	−0.9	−0.7	4.35	0.09	0.68
No. of H-bonds^†		410	445	468	332	481	513
R-work		0.2248	0.3515	0.2423 (0.2395)^‡	0.2529	0.3404	0.2531 (0.2506)^‡
R-free		0.2704	0.3760	0.2726 (0.2802)^‡	0.3128	0.3863	0.2857 (0.3107)^‡
Map correlation		0.8	0.7	0.75	0.68	0.59	0.68
RMSD from ideal	Bond length (Å)	0.029	0.039	0.035	0.012	0.036	0.026
RMSD from ideal	Angle (°)	2.659	3.162	2.831	1.579	2.125	2.093
RamaMap statistics (%)
Preferred^§		83	91	91	85	91	91
Allowed		11	5	6	10	6	6
Outliers		6	4	4	5	2	3

Protein		A-DNA-binding protein			A-Protein-lipid complex
		Initial	TOP^∗		Initial	TOP^∗
		Initial	Stage 1	Stage 2	Initial	Stage 1	Stage 2
Resolution		3.35–20.0			2.60–43.5 Å
No. of residues		364			376
Starting model		Early stage			Final stage (3OV6)
C_α-RMSD (Å)		N/A	0.85	0.97	N/A	0.74	0.32
<TSP>		3.33	−2.0	−1.5	2.92	−0.1	0.13
No. of H-bonds^†		147	187	192	168	181	193
R-work		0.2890	0.3874	0.3136 (0.3079)^‡	0.2285	0.3611	0.2323 (0.2341) ^‡
R-free		0.3722	0.4418	0.3562 (0.3830)	0.2851	0.4076	0.2551 (0.2760)
Map correlation		0.75	0.68	0.74	0.88	0.78	0.86
RMSD from ideal	Bond length (Å)	0.007	0.014	0.016	0.009	0.026	0.017
RMSD from ideal	Angle (°)^‡	1.218	1.689	1.837	1.401	2.147	1.944
RamaMap statistics (%)
Preferred^§		81	94	94	93	94	95
Allowed		11	3	3	5	4	3
Outliers		8	3	3	1	2	2

^∗

Stage 1 and Stage 2 refer to backbone refinement using the MCSA/double-crank algorithm and all-atom energy minimization using the electron density, respectively.

^†

Backbone H-bonds are defined when the amide nitrogen and carbonyl oxygen are within 3.5 Å and the angle between the N-H and O=C bond vectors exceeds 145°.

^‡

The values in parentheses are the R and R-free values calculated where the more stringent maps generated after excluding the free reflections are used in the real-space refinement stage of TOP.

^§

As defined by the program COOT (36).