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CRYSTAL STRUCTURE OF NITRIC OXIDE TREATED 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 2.74 55.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.275 α = 90 b = 128.275 β = 90 c = 86.348 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 EIGER X 16M 2019-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.86999 Diamond I03
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 1.17 37.057 97.2 0.063 0.07 0.032 0.999 10.3 4.7 173732
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 1.17 1.19 73.2 0.853 1.043 0.588 0.504 1 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 (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 1.17 37.057 173704 8589 97.174 0.106 0.1052 0.1052 0.1274 0.1274 RANDOM 16.042
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] 0.111 0.056 0.111 -0.362
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.226 r_dihedral_angle_6_deg 16.125 r_lrange_other 13.622 r_dihedral_angle_3_deg 11.142 r_dihedral_angle_2_deg 8.199 r_dihedral_angle_1_deg 7.02 r_scangle_it 6.684 r_scangle_other 6.684 r_mcangle_other 4.772 r_mcangle_it 4.771
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.226 r_dihedral_angle_6_deg 16.125 r_lrange_other 13.622 r_dihedral_angle_3_deg 11.142 r_dihedral_angle_2_deg 8.199 r_dihedral_angle_1_deg 7.02 r_scangle_it 6.684 r_scangle_other 6.684 r_mcangle_other 4.772 r_mcangle_it 4.771 r_scbond_other 4.735 r_scbond_it 4.734 r_mcbond_it 3.394 r_rigid_bond_restr 3.369 r_mcbond_other 3.364 r_angle_refined_deg 1.804 r_angle_other_deg 0.68 r_symmetry_xyhbond_nbd_refined 0.271 r_nbd_refined 0.259 r_nbd_other 0.216 r_symmetry_nbd_refined 0.215 r_xyhbond_nbd_refined 0.212 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.175 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.085 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_gen_planes_other 0.007 r_metal_ion_refined 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3437 Nucleic Acid Atoms Solvent Atoms 775 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction Coot model building REFMAC phasing