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1.20 A resolution crystal structure of dioxygen bound copper-containing nitrite reductase from Geobacillus thermodenitrificans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WKO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 0.1M sodium acetate, 5.5%(w/v) PEG 4000, 0.075M CuSO4 , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3 59.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.903 α = 90 b = 114.903 β = 90 c = 84.022 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 2013-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 0.96 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.2 100 92.1 0.075 3.5 120357 120357 4 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 96.8 0.263 3 3.3 6323
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 3WKO 1.2 28.73 114262 114262 6088 91.86 0.12085 0.12085 0.1195 0.1161 0.14627 0.1449 RANDOM 15.588
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.787 r_sphericity_free 42.128 r_sphericity_bonded 19.288 r_dihedral_angle_3_deg 13.026 r_rigid_bond_restr 10.497 r_dihedral_angle_4_deg 9.195 r_dihedral_angle_1_deg 8.153 r_angle_refined_deg 2.439 r_chiral_restr 0.169 r_bond_refined_d 0.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.787 r_sphericity_free 42.128 r_sphericity_bonded 19.288 r_dihedral_angle_3_deg 13.026 r_rigid_bond_restr 10.497 r_dihedral_angle_4_deg 9.195 r_dihedral_angle_1_deg 8.153 r_angle_refined_deg 2.439 r_chiral_restr 0.169 r_bond_refined_d 0.031 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2314 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 56
Software Software Software Name Purpose SERGUI data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling