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Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 16.7 MGy
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M sodium acetate, 5.5%(w/v) PEG4000, 0.075M CuSO4
Crystal Properties Matthews coefficient Solvent content 3.03 59.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.098 α = 90 b = 115.098 β = 90 c = 84.305 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 96.4 10 2.9 64668
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 33.23 61383 3276 96.35 0.14976 0.14754 0.1472 0.19185 0.1914 RANDOM 15.965
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] 0.02 0.01 0.02 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.314 r_sphericity_free 32.069 r_dihedral_angle_3_deg 13.079 r_sphericity_bonded 9.394 r_dihedral_angle_1_deg 7.877 r_dihedral_angle_4_deg 5.679 r_rigid_bond_restr 4.625 r_long_range_B_refined 4.483 r_long_range_B_other 4.011 r_scangle_other 3.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.314 r_sphericity_free 32.069 r_dihedral_angle_3_deg 13.079 r_sphericity_bonded 9.394 r_dihedral_angle_1_deg 7.877 r_dihedral_angle_4_deg 5.679 r_rigid_bond_restr 4.625 r_long_range_B_refined 4.483 r_long_range_B_other 4.011 r_scangle_other 3.933 r_scbond_it 3.563 r_scbond_other 3.497 r_mcangle_other 2.696 r_mcangle_it 2.686 r_mcbond_it 2.412 r_mcbond_other 2.244 r_angle_refined_deg 1.937 r_angle_other_deg 0.875 r_chiral_restr 0.125 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 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 301 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing