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Crystal structure of as isolated synthetic core domain of nitrite reductase from Ralstonia pickettii (residues 1-331)
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 6 297 containing 0.2 MgCl2, 20% P6000 in MES buffer pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.35 47.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.884 α = 90 b = 167.52 β = 90 c = 143.982 γ = 90
Symmetry Space Group C 2 2 21
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 R 4M 2018-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.25 45.6 94.4 0.11 0.076 0.994 9.3 3.8 84912 25.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.3 75.4 0.75 0.53 0.541 1.4 3.4
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 MOLECULAR REPLACEMENT THROUGHOUT 3ziy 2.25 42.68 84912 4426 94.12 0.1817 0.17884 0.1843 0.23698 0.2369 RANDOM 30.131
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] 0.58 -1.12 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.405 r_dihedral_angle_4_deg 19.23 r_dihedral_angle_3_deg 15.26 r_dihedral_angle_1_deg 9.075 r_long_range_B_other 3.529 r_long_range_B_refined 3.528 r_scangle_other 1.728 r_mcangle_it 1.486 r_mcangle_other 1.485 r_angle_refined_deg 1.443
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.405 r_dihedral_angle_4_deg 19.23 r_dihedral_angle_3_deg 15.26 r_dihedral_angle_1_deg 9.075 r_long_range_B_other 3.529 r_long_range_B_refined 3.528 r_scangle_other 1.728 r_mcangle_it 1.486 r_mcangle_other 1.485 r_angle_refined_deg 1.443 r_angle_other_deg 1.203 r_scbond_other 1 r_scbond_it 0.999 r_mcbond_it 0.869 r_mcbond_other 0.869 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14615 Nucleic Acid Atoms Solvent Atoms 1062 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing