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Crystal structure of as isolated Y323E 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 2.75 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.55 α = 90 b = 127.55 β = 90 c = 172.68 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 PILATUS 6M mirrors 2018-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97857 SOLEIL PROXIMA 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 1.45 46.64 98.5 0.054 0.05 0.99 8.8 2.8 183931
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 1.45 1.49 95.2 1.167 0.905 0.428 0.8 2.5
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 1.65 42.73 118437 6234 98.85 0.15937 0.15838 0.1714 0.17806 0.1883 RANDOM 20.555
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] 0.83 0.42 0.83 -2.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.145 r_dihedral_angle_4_deg 21.092 r_dihedral_angle_3_deg 12.668 r_dihedral_angle_1_deg 7.302 r_long_range_B_refined 5.851 r_long_range_B_other 5.499 r_scangle_other 2.074 r_angle_refined_deg 1.671 r_angle_other_deg 1.45 r_mcangle_it 1.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.145 r_dihedral_angle_4_deg 21.092 r_dihedral_angle_3_deg 12.668 r_dihedral_angle_1_deg 7.302 r_long_range_B_refined 5.851 r_long_range_B_other 5.499 r_scangle_other 2.074 r_angle_refined_deg 1.671 r_angle_other_deg 1.45 r_mcangle_it 1.283 r_mcangle_other 1.283 r_scbond_it 1.282 r_scbond_other 1.282 r_mcbond_it 0.773 r_mcbond_other 0.773 r_chiral_restr 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.006 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 6859 Nucleic Acid Atoms Solvent Atoms 1165 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing