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Crystal Structure of Copper Nitrite Reductase at 100K after 7.59 MGy
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BWI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 4.5 298 1.7 M Ammonium Sulphate, 0.1 M Sodium Acetate pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.02 38.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.155 α = 90 b = 95.155 β = 90 c = 95.155 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2013-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.09 42.6 97.5 0.042 0.048 0.022 0.999 15.9 4 115628
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.09 1.11 96.8 0.925 1.097 0.578 0.559 3.3 5650
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 2BWI 1.09 42.6 109866 5751 97.07 0.1276 0.1267 0.1463 0.1483 RANDOM 14.488
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 35.59 r_sphericity_free 32.364 r_dihedral_angle_4_deg 18.181 r_dihedral_angle_3_deg 12.43 r_dihedral_angle_1_deg 8.062 r_sphericity_bonded 7.835 r_rigid_bond_restr 2.103 r_angle_refined_deg 1.731 r_mcangle_it 1.552 r_mcbond_it 1.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.59 r_sphericity_free 32.364 r_dihedral_angle_4_deg 18.181 r_dihedral_angle_3_deg 12.43 r_dihedral_angle_1_deg 8.062 r_sphericity_bonded 7.835 r_rigid_bond_restr 2.103 r_angle_refined_deg 1.731 r_mcangle_it 1.552 r_mcbond_it 1.251 r_mcbond_other 1.238 r_angle_other_deg 1.049 r_chiral_restr 0.113 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2566 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing