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Nitrite-bound thermostable copper nitrite reductase at 320 K
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 5.5% PEG 4000, 0.1M sodium acetate, 0.075M copper sulphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.9 57.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.3 α = 90 b = 116.3 β = 90 c = 85.652 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 320 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 1.00000 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 1.55 50 96.6 0.066 3.9 60565
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 1.55 1.58 98.9 0.377 2.5 3.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3WKO 1.55 34.79 57494 3063 96.6 0.11539 0.11454 0.1292 0.13141 0.1446 RANDOM 24.242
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.907 r_dihedral_angle_3_deg 14.787 r_dihedral_angle_4_deg 13.597 r_dihedral_angle_1_deg 7.851 r_long_range_B_refined 6.409 r_sphericity_bonded 6.393 r_long_range_B_other 6.284 r_scangle_other 5.067 r_scbond_it 3.432 r_scbond_other 3.395
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.907 r_dihedral_angle_3_deg 14.787 r_dihedral_angle_4_deg 13.597 r_dihedral_angle_1_deg 7.851 r_long_range_B_refined 6.409 r_sphericity_bonded 6.393 r_long_range_B_other 6.284 r_scangle_other 5.067 r_scbond_it 3.432 r_scbond_other 3.395 r_mcangle_it 2.899 r_mcangle_other 2.898 r_angle_refined_deg 2.365 r_mcbond_it 2.064 r_mcbond_other 2.064 r_angle_other_deg 0.947 r_chiral_restr 0.142 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2313 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 9
Software Software Software Name Purpose BSS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling