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CRYSTAL STRUCTURE OF AS-ISOLATED F295L 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 2.81 56.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.257 α = 90 b = 128.257 β = 90 c = 86.194 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 2021-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.8000 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 1.16 32.085 99.5 0.088 0.103 0.052 0.996 5.8 3.6 182213
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 1.16 1.18 99.8 0.993 1.176 0.619 0.433 3.5
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 (All) 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 1.16 32.085 182147 9199 99.478 0.116 0.1143 0.1143 0.139 0.1389 RANDOM 17.911
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] 0.687 0.344 0.687 -2.229
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 20.69 r_dihedral_angle_6_deg 16.264 r_lrange_other 16.085 r_dihedral_angle_3_deg 11.198 r_dihedral_angle_2_deg 9.756 r_scangle_it 8.945 r_scangle_other 8.945 r_dihedral_angle_1_deg 6.871 r_scbond_other 6.613 r_scbond_it 6.611
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 20.69 r_dihedral_angle_6_deg 16.264 r_lrange_other 16.085 r_dihedral_angle_3_deg 11.198 r_dihedral_angle_2_deg 9.756 r_scangle_it 8.945 r_scangle_other 8.945 r_dihedral_angle_1_deg 6.871 r_scbond_other 6.613 r_scbond_it 6.611 r_mcangle_other 5.691 r_mcangle_it 5.69 r_rigid_bond_restr 4.533 r_mcbond_it 4.306 r_mcbond_other 4.244 r_angle_refined_deg 1.957 r_angle_other_deg 0.703 r_symmetry_xyhbond_nbd_refined 0.24 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.229 r_nbd_other 0.206 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.177 r_symmetry_nbd_refined 0.17 r_chiral_restr 0.109 r_symmetry_nbtor_other 0.088 r_symmetry_xyhbond_nbd_other 0.046 r_bond_refined_d 0.015 r_symmetry_metal_ion_refined 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3432 Nucleic Acid Atoms Solvent Atoms 763 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction Coot model building REFMAC phasing