Table 2.

DEN Refinement Improves Low Resolution Structures in the PDB^a

			Rfree			Rfree-Rwork		Ramachandran Score
PDB Identifier	Resolution(Å)	Number Residues	DEN	noDEN	Improvement	DEN	noDEN	DEN	noDEN	Improvement	Comments
1av1	4.00	804	0.335	0.336	0.0012	0.07	0.07	0.840	0.872	−0.0314
1isr	4.00	448	0.233	0.237	0.0043	0.07	0.07	0.833	0.833	0.0000
1jl4	4.30	557	0.353	0.354	0.0009	0.12	0.11	0.718	0.705	0.0127
1pgf	4.50	1102	0.284	0.295	0.0108	0.08	0.11	0.856	0.804	0.0519	Small differences throughout
1r5u	4.50	3517	0.334	0.335	0.0003	0.05	0.05	0.714	0.710	0.0046
1xdv	4.10	1517	0.358	0.367	0.0089	0.12	0.11	0.780	0.783	−0.0034
1xxi	4.10	3532	0.407	0.465	0.0582	0.05	0.12	0.842	0.612	0.2301	Large differences (~ 4 A domain motions)
1ye1	4.50	574	0.312	0.350	0.0381	0.08	0.15	0.894	0.705	0.1890	Small differences throughout
1yi5	4.20	1356	0.323	0.336	0.0139	0.07	0.09	0.758	0.709	0.0497	Local differences in several chains
1z9j	4.50	821	0.317	0.331	0.0135	0.07	0.09	0.838	0.762	0.0761	Large differences in chain A (domain motion)
2a62	4.50	319	0.340	0.353	0.0131	0.07	0.09	0.590	0.606	−0.0159
2bf1	4.00	304	0.479	0.492	0.0131	0.12	0.12	0.467	0.507	−0.0400
2i36	4.10	962	0.387	0.401	0.0137	0.02	0.03	0.839	0.687	0.1520	Local difference in chain B
2qag	4.00	702	0.392	0.401	0.0091	0.02	0.02	0.616	0.614	0.0016
2vkz	4.00	10941	0.327	0.337	0.0095	0.05	0.07	0.832	0.762	0.0692	Large differences in subdomain placements
3bbw	4.00	543	0.304	0.334	0.0304	0.01	0.04	0.876	0.776	0.0998	Significant local difference
3crw	4.00	485	0.324	0.338	0.0136	0.09	0.11	0.836	0.777	0.0589	Large difference in one domain (hinge motion)
3dmk	4.19	2127	0.407	0.428	0.0211	0.08	0.11	0.742	0.653	0.0896	Differences throughout, reference model only 50%
3du7	4.10	1839	0.332	0.336	0.0039	0.09	0.09	0.730	0.707	0.0225
Average	4.19	1708	0.345	0.359	0.0146	0.07	0.09	0.768	0.715	0.0535
Minimum	4.00	304	0.233	0.237	0.0003	0.01	0.02	0.467	0.507	−0.0400
Maximum	4.50	10941	0.479	0.492	0.0582	0.12	0.15	0.894	0.872	0.2301

^aNineteen PDB structures were re-refined with and without DEN (Online Methods). The tested proteins show a wide range of sizes extending from 304 residues for 2bf1 to 10941 residues for 1vkz. The final R_free, R_free − R_work values, as well as Ramachandran Scores are shown. In all cases, DEN refinement shows improvement of R_free as compared to noDEN; eleven out of nineteen cases show an R_free improvement that is larger than 0.01. In fifteen of the nineteen cases DEN refinement also improves the Ramachandran Score (four exceptions are 2bf1, 1av1, 2a62 and 1xdv). As would be expected R_free is larger than R_work (the R-factor that was optimized) with average differences of 0.07 and 0.09 for DEN and noDEN refinement, respectively. In each column, green shading marks the most favorable maximum or minimum value (high Ramachandran Score or low R-value);

pink shading marks the least favorable value. The comments refer to the differences between the reference models and the corresponding DEN-refined crystal structures for the cases with γ<1 (cf. Supplementary Table 4). Two particular examples of these differences are shown in Supplementary Fig. 5.