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H294M mutant of copper-containing nitrite reductase from Geobacillus thermodenitrificans showing two coordination geometries at the T2Cu site
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 2.82 56.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.275 α = 90 b = 115.275 β = 90 c = 84.691 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 ADSC QUANTUM 315 2013-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.75000 SPring-8 BL38B1
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 1.3 50 99.9 0.069 11.3 3.8 102895
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 1.3 1.37 99.5 0.573 2.3 3.7 14968
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3WKO 1.3 28.82 97746 5147 99.95 0.10686 0.10573 0.12809 0.1395 RANDOM 13.278
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 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.383 r_sphericity_free 29.058 r_dihedral_angle_3_deg 11.368 r_sphericity_bonded 9.131 r_dihedral_angle_4_deg 8.617 r_dihedral_angle_1_deg 8.155 r_rigid_bond_restr 5.516 r_long_range_B_refined 3.734 r_long_range_B_other 3.241 r_scangle_other 2.996
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.383 r_sphericity_free 29.058 r_dihedral_angle_3_deg 11.368 r_sphericity_bonded 9.131 r_dihedral_angle_4_deg 8.617 r_dihedral_angle_1_deg 8.155 r_rigid_bond_restr 5.516 r_long_range_B_refined 3.734 r_long_range_B_other 3.241 r_scangle_other 2.996 r_scbond_it 2.974 r_scbond_other 2.973 r_angle_refined_deg 2.057 r_mcangle_it 1.809 r_mcangle_other 1.808 r_mcbond_it 1.574 r_mcbond_other 1.405 r_angle_other_deg 0.904 r_chiral_restr 0.13 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 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 2295 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 22
Software Software Software Name Purpose BSS data collection MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling