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CRYSTAL STRUCTURE OF AS-ISOLATED Q262N MUTANT OF THREE-DOMAIN HEME-CU NITRITE REDUCTASE FROM RALSTONIA PICKETTII
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZIY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.7 277 100 mM bis-tris propane pH 7.7, 200 mM sodium citrate, and 22% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.68 54.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.65 α = 90 b = 127.65 β = 90 c = 86.29 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 6M Mirrors 2021-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.99990 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.5 37.63 100 0.108 0.121 0.054 0.996 8.3 5 83956
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 100 1.324 1.481 0.659 0.431 1.2 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 FOURIER SYNTHESIS THROUGHOUT 3ZIY 1.5 37.63 79820 4134 99.97 0.1076 0.1054 0.1008 0.1528 0.1508 RANDOM 24.346
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] 1.41 0.71 1.41 -4.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.14 r_dihedral_angle_4_deg 21.359 r_dihedral_angle_3_deg 13.403 r_dihedral_angle_1_deg 7.11 r_rigid_bond_restr 4.523 r_angle_refined_deg 2.052 r_angle_other_deg 0.691 r_chiral_restr 0.131 r_bond_refined_d 0.018 r_gen_planes_refined 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.14 r_dihedral_angle_4_deg 21.359 r_dihedral_angle_3_deg 13.403 r_dihedral_angle_1_deg 7.11 r_rigid_bond_restr 4.523 r_angle_refined_deg 2.052 r_angle_other_deg 0.691 r_chiral_restr 0.131 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3439 Nucleic Acid Atoms Solvent Atoms 639 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction xia2 data reduction AutoProcess phasing