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As-isolated resting state copper nitrite reductase from Achromobacter xylosoxidans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OE1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 10% w/v PEG 550 MME, 10 mM ZnSO4, 100 mM MES buffer, pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.07 59.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.347 α = 90 b = 90.347 β = 90 c = 143.58 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 6M 2016-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 47.86 98 0.147 0.981 5.1 3.3 56521
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 97.8 0.55 0.782 3.1
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 1oe1 1.6 47.86 53635 2884 98 0.19141 0.18964 0.1933 0.22334 0.2212 RANDOM 28.144
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] 0.59 0.3 0.59 -1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.361 r_dihedral_angle_4_deg 17.035 r_dihedral_angle_3_deg 14.231 r_dihedral_angle_1_deg 7.643 r_long_range_B_refined 5.313 r_long_range_B_other 5.134 r_scangle_other 3.992 r_mcangle_other 2.929 r_mcangle_it 2.924 r_scbond_it 2.858
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.361 r_dihedral_angle_4_deg 17.035 r_dihedral_angle_3_deg 14.231 r_dihedral_angle_1_deg 7.643 r_long_range_B_refined 5.313 r_long_range_B_other 5.134 r_scangle_other 3.992 r_mcangle_other 2.929 r_mcangle_it 2.924 r_scbond_it 2.858 r_scbond_other 2.857 r_mcbond_it 2.209 r_mcbond_other 2.183 r_angle_refined_deg 1.897 r_angle_other_deg 1.036 r_chiral_restr 0.116 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2567 Nucleic Acid Atoms Solvent Atoms 378 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing