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Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 8.38 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 3.01 59.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.951 α = 90 b = 114.951 β = 90 c = 84.225 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 96.6 11.2 2.9 64868
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 34.35 61582 3286 96.49 0.14266 0.14029 0.141 0.18732 0.1874 RANDOM 18.561
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 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.511 r_sphericity_free 36.63 r_dihedral_angle_3_deg 12.397 r_sphericity_bonded 10.512 r_dihedral_angle_1_deg 8.099 r_dihedral_angle_4_deg 6.597 r_long_range_B_refined 5.107 r_rigid_bond_restr 5.068 r_long_range_B_other 4.469 r_scangle_other 4.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.511 r_sphericity_free 36.63 r_dihedral_angle_3_deg 12.397 r_sphericity_bonded 10.512 r_dihedral_angle_1_deg 8.099 r_dihedral_angle_4_deg 6.597 r_long_range_B_refined 5.107 r_rigid_bond_restr 5.068 r_long_range_B_other 4.469 r_scangle_other 4.082 r_scbond_it 3.888 r_scbond_other 3.778 r_mcangle_other 2.882 r_mcangle_it 2.874 r_mcbond_it 2.444 r_mcbond_other 2.342 r_angle_refined_deg 1.908 r_angle_other_deg 0.901 r_chiral_restr 0.131 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2293 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing