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Neutron and X-ray joint refined structure of a copper-containing nitrite reductase (C135A mutant) in complex with formate
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YSO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 0.1 M acetate buffer pH 4.5, 5.5% (w/v) PEG 4000, and 75 mM CuSO4
Crystal Properties Matthews coefficient Solvent content 3.13 60.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.172 α = 90 b = 116.172 β = 90 c = 85.612 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 neutron 298 DIFFRACTOMETER iBIX 2021-05-13 L LAUE 2 1 x-ray 298 PIXEL DECTRIS PILATUS3 S 6M 2021-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SPALLATION SOURCE J-PARC MLF BEAMLINE BL-03 2.44-5.28 JPARC MLF BL-03 2 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 1.9 20 97.7 0.264 0.108 0.975 6.5 6.8 33212 12.78 2 1.2 43.4 100 0.088 0.021 0.996 9.7 5.1 134752 12.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 0.89 0.428 0.527 1.7 5.1 2 1.2 1.22 0.9 0.253 0.701 1.7 5
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MOLECULAR REPLACEMENT 1.2 39.39 1.97 134742 3999 99.98 0.1141 0.1139 0.113 0.1185 0.1184 30 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 1.9 12.9 33208 96.94 0.146 0.183
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 f_dihedral_angle_d 16.5797 f_angle_d 1.1745 f_chiral_restr 0.0908 f_bond_d 0.0217 f_plane_restr 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2335 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 7
Software Software Software Name Purpose PHENIX refinement STARGazer data reduction XDS data reduction SCALA data scaling MOLREP phasing