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Crystal structure of a putative nitroreductase in complex with fmn (dde_0787) from desulfovibrio desulfuricans subsp. at 1.70 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 277 40.0000% PEG-400, 0.1M Acetate pH 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.07 40.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.78 α = 90 b = 67.99 β = 90 c = 99.74 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315 Vertical focusing mirror 2008-07-22 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.918370,0.979421,0.979155 SSRL BL9-1
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 1.7 28.094 96.9 0.078 8.85 36111 -3 13.566
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) 1.7 1.76 99 0.461 1.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.7 28.094 36077 1806 98.96 0.166 0.165 0.1711 0.201 0.2047 RANDOM 10.969
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] 0.59 0.34 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.633 r_dihedral_angle_3_deg 10.441 r_dihedral_angle_4_deg 10.254 r_scangle_it 5.229 r_dihedral_angle_1_deg 4.117 r_scbond_it 3.766 r_mcangle_it 2.44 r_mcbond_it 1.856 r_angle_refined_deg 1.524 r_angle_other_deg 0.983
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.633 r_dihedral_angle_3_deg 10.441 r_dihedral_angle_4_deg 10.254 r_scangle_it 5.229 r_dihedral_angle_1_deg 4.117 r_scbond_it 3.766 r_mcangle_it 2.44 r_mcbond_it 1.856 r_angle_refined_deg 1.524 r_angle_other_deg 0.983 r_mcbond_other 0.478 r_symmetry_vdw_other 0.284 r_nbd_refined 0.221 r_nbd_other 0.216 r_nbtor_refined 0.176 r_symmetry_hbond_refined 0.171 r_xyhbond_nbd_refined 0.157 r_symmetry_vdw_refined 0.127 r_chiral_restr 0.097 r_nbtor_other 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2664 Nucleic Acid Atoms Solvent Atoms 373 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing