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Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 25.0 MGy
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
Crystal Properties Matthews coefficient Solvent content 3.03 59.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.213 α = 90 b = 115.213 β = 90 c = 84.385 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 MX225HE 2014-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 0.75000 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 50 96.1 8.05 2.8 64638
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.5 42.94 61355 3274 96.08 0.16514 0.16285 0.1626 0.20829 0.2082 RANDOM 15.832
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 43.188 r_sphericity_free 31.276 r_dihedral_angle_3_deg 13.172 r_sphericity_bonded 9.322 r_dihedral_angle_1_deg 7.979 r_dihedral_angle_4_deg 5.491 r_rigid_bond_restr 5.248 r_long_range_B_refined 4.689 r_long_range_B_other 4.117 r_scangle_other 3.724
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.188 r_sphericity_free 31.276 r_dihedral_angle_3_deg 13.172 r_sphericity_bonded 9.322 r_dihedral_angle_1_deg 7.979 r_dihedral_angle_4_deg 5.491 r_rigid_bond_restr 5.248 r_long_range_B_refined 4.689 r_long_range_B_other 4.117 r_scangle_other 3.724 r_scbond_it 3.5 r_scbond_other 3.436 r_mcangle_it 2.683 r_mcangle_other 2.682 r_mcbond_other 2.422 r_mcbond_it 2.421 r_angle_refined_deg 2.008 r_angle_other_deg 0.884 r_chiral_restr 0.129 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2293 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing