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Crystal structure of nitrite bound synthetic core domain of nitrite reductase from Ralstonia pickettii (residues 1-331)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 284 0.2 MgCl2, 20% P6000 in MES buffer pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.35 47.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.91 α = 90 b = 167.553 β = 90 c = 143.973 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS EIGER X 16M Mirrors 2018-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.89 83 99.9 0.21 0.09 0.99 5.3 6.75 159198 34.11
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.92 99.7 1.25 0.52 0.485 0.9 6.57
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 MOLECULAR REPLACEMENT THROUGHOUT 1.9 50.01 149138 7566 99.86 0.18048 0.17834 0.186 0.22377 0.2279 RANDOM 26.74
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.116 r_dihedral_angle_4_deg 19.889 r_dihedral_angle_3_deg 13.391 r_dihedral_angle_1_deg 8.689 r_long_range_B_refined 4.53 r_long_range_B_other 4.53 r_angle_refined_deg 1.373 r_angle_other_deg 1.259 r_scangle_other 1.217 r_mcangle_it 1.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.116 r_dihedral_angle_4_deg 19.889 r_dihedral_angle_3_deg 13.391 r_dihedral_angle_1_deg 8.689 r_long_range_B_refined 4.53 r_long_range_B_other 4.53 r_angle_refined_deg 1.373 r_angle_other_deg 1.259 r_scangle_other 1.217 r_mcangle_it 1.042 r_mcangle_other 1.041 r_scbond_it 0.732 r_scbond_other 0.732 r_mcbond_it 0.616 r_mcbond_other 0.615 r_chiral_restr 0.056 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14602 Nucleic Acid Atoms Solvent Atoms 1849 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing