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Crystal structure of putative nitroreductase ydfN (2632848) from Bacillus subtilis at 1.65 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 277 NANODROP, 40.0% 1,2-propanediol, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.14 42.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.62 α = 90 b = 69.2 β = 100.54 c = 61.85 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD Adjustable focusing mirrors in K-B geometry 2007-10-26 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.91840, 0.97939, 0.97953 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.65 28.583 97 0.051 8.98 51334 -3 27.797
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.71 89.9 0.291 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.65 28.583 51310 2620 99.4 0.152 0.151 0.175 0.1886 RANDOM 17.273
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.34 -0.4 0.09 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.588 r_dihedral_angle_4_deg 14.714 r_dihedral_angle_3_deg 13.864 r_scangle_it 7.211 r_dihedral_angle_1_deg 5.984 r_scbond_it 5.078 r_mcangle_it 3.069 r_mcbond_it 2.433 r_angle_refined_deg 1.61 r_angle_other_deg 0.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.588 r_dihedral_angle_4_deg 14.714 r_dihedral_angle_3_deg 13.864 r_scangle_it 7.211 r_dihedral_angle_1_deg 5.984 r_scbond_it 5.078 r_mcangle_it 3.069 r_mcbond_it 2.433 r_angle_refined_deg 1.61 r_angle_other_deg 0.997 r_mcbond_other 0.57 r_symmetry_vdw_refined 0.327 r_symmetry_hbond_refined 0.246 r_nbd_refined 0.228 r_symmetry_vdw_other 0.217 r_nbd_other 0.2 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.154 r_xyhbond_nbd_other 0.107 r_chiral_restr 0.094 r_nbtor_other 0.088 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3276 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction