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Crystal structure of nitrite bound Y323A mutant of haem-Cu containing nitrite reductase from Ralstonia pickettii
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 283 0.1M HEPES (pH7.5), 20% PEG 3350, 0.2 M Sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.74 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.5 α = 90 b = 128.5 β = 90 c = 172.47 γ = 120
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 PILATUS3 S 6M 2018-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96861 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.61 30.1 99.8 0.142 0.071 0.997 5 137234 14.878
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 1.61 1.64 99.9 1.8 0.89 0.448 5
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 THROUGHOUT 1.7 29.33 111132 5447 99.75 0.17518 0.1738 0.1845 0.20303 0.2099 RANDOM 20.427
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] 0.19 0.1 0.19 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.057 r_dihedral_angle_4_deg 21.566 r_dihedral_angle_3_deg 13.037 r_dihedral_angle_1_deg 7.266 r_long_range_B_refined 5.98 r_long_range_B_other 5.461 r_scangle_other 1.838 r_angle_refined_deg 1.509 r_angle_other_deg 1.363 r_mcangle_it 1.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.057 r_dihedral_angle_4_deg 21.566 r_dihedral_angle_3_deg 13.037 r_dihedral_angle_1_deg 7.266 r_long_range_B_refined 5.98 r_long_range_B_other 5.461 r_scangle_other 1.838 r_angle_refined_deg 1.509 r_angle_other_deg 1.363 r_mcangle_it 1.228 r_mcangle_other 1.228 r_scbond_it 1.13 r_scbond_other 1.129 r_mcbond_it 0.74 r_mcbond_other 0.737 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 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 6839 Nucleic Acid Atoms Solvent Atoms 1174 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing