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Crystal structure of nitrite bound Y323F mutant of haem-Cu containing nitrite reductase from Ralstonia pickettii
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 284 0.1M HEPES (pH7.5), 20% PEG 3350, 0.2 M Sodium citrate
Crystal Properties Matthews coefficient Solvent content 4.96 75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.975 α = 90 b = 180.975 β = 90 c = 180.975 γ = 90
Symmetry Space Group I 21 3
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 6M mirrors 2018-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 2.6 73.88 92.9 0.138 0.104 0.973 5.5 2.9 27909 36.3
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 2.6 2.72 97 0.634 0.496 0.548 1.8 2.8
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 THROUGHOUT 2.6 73 26486 1423 91.78 0.15379 0.15192 0.1592 0.18876 0.1917 RANDOM 40.4
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.686 r_dihedral_angle_4_deg 20.853 r_dihedral_angle_3_deg 16.19 r_long_range_B_refined 8.237 r_long_range_B_other 8.214 r_dihedral_angle_1_deg 7.85 r_scangle_other 6.667 r_mcangle_it 4.886 r_mcangle_other 4.886 r_scbond_it 4.477
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.686 r_dihedral_angle_4_deg 20.853 r_dihedral_angle_3_deg 16.19 r_long_range_B_refined 8.237 r_long_range_B_other 8.214 r_dihedral_angle_1_deg 7.85 r_scangle_other 6.667 r_mcangle_it 4.886 r_mcangle_other 4.886 r_scbond_it 4.477 r_scbond_other 4.472 r_mcbond_it 3.316 r_mcbond_other 3.293 r_angle_refined_deg 1.74 r_angle_other_deg 1.266 r_chiral_restr 0.067 r_bond_refined_d 0.01 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 3424 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing