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High-resolution neutron and X-ray joint refined structure of copper-containing nitrite reductase from Geobacillus thermodenitrificans
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 4.6 293 0.1 M acetate buffer pH 4.6, 5.5% (w/v) PEG 4000, and 50 mM CuSO4
Crystal Properties Matthews coefficient Solvent content 2.96 58.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.212 α = 90 b = 114.212 β = 90 c = 83.688 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 PILATUS 2M-F 2018-12-16 M SINGLE WAVELENGTH 2 1 neutron 100 DIFFRACTOMETER iBIX 2018-11-26 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A 2 SPALLATION SOURCE J-PARC MLF BEAMLINE BL-03 2.15-4.89 JPARC MLF BL-03
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 1.03 42.58 99.9 0.065 0.021 21.2 9.6 201251 2 1.5 17.38 99.7 0.23 0.097 9.5 6.6 64997 6.1
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 1.03 1.05 0.641 0.253 0.907 3.5 7.1 2 1.5 1.59 0.608 0.285 0.782 2.2 5.3
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 1.3 34.13 2 100127 2516 100 0.0978 0.0973 0.0978 0.1117 0.1119 15.48 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 1.5 17.071 64964 2006 99.69 0.1421 0.1416 0.1586
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 21.0391 f_dihedral_angle_d 21.0391 f_angle_d 1.0535 f_angle_d 1.0535 f_chiral_restr 0.0904 f_chiral_restr 0.0904 f_bond_d 0.008 f_bond_d 0.008 f_plane_restr 0.0075 f_plane_restr 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2314 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction STARGazer data reduction