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Structure of copper-containing nitrite reductase from Geobacillus thermodenitrificans without chloride
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WKO PDB ENTRY 3WKO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 0.1 M acetate buffer, 5.0%(w/v) PEG 4000, 75 mM CuSO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.78 55.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.88 α = 90 b = 114.88 β = 90 c = 84.233 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 CCD RAYONIX MX300HE 2014-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.25 50 99.9 0.114 16.5 7.5 114829
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.29 99.9 0.37 3.6 5.7 11494
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 PDB ENTRY 3WKO 1.25 34.34 109065 5758 99.82 0.14216 0.14063 0.1417 0.17072 0.1717 RANDOM 13.924
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] -0.03 -0.02 -0.03 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.783 r_sphericity_free 34.92 r_dihedral_angle_3_deg 13.105 r_sphericity_bonded 10.287 r_dihedral_angle_1_deg 8.207 r_dihedral_angle_4_deg 7.609 r_rigid_bond_restr 5.33 r_long_range_B_refined 4.943 r_long_range_B_other 4.179 r_scbond_it 4.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.783 r_sphericity_free 34.92 r_dihedral_angle_3_deg 13.105 r_sphericity_bonded 10.287 r_dihedral_angle_1_deg 8.207 r_dihedral_angle_4_deg 7.609 r_rigid_bond_restr 5.33 r_long_range_B_refined 4.943 r_long_range_B_other 4.179 r_scbond_it 4.005 r_scangle_other 3.966 r_scbond_other 3.941 r_mcangle_other 2.252 r_mcangle_it 2.235 r_mcbond_it 2.13 r_angle_refined_deg 2.112 r_mcbond_other 2.076 r_angle_other_deg 0.925 r_chiral_restr 0.129 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2293 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 30
Software Software Software Name Purpose BSS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling