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Crystal Structure of Copper Nitrite Reductase at 100K after 2.76 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 1.98 37.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.299 α = 90 b = 95.299 β = 90 c = 95.299 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 1.08 42.62 97.4 0.046 0.052 0.024 0.999 14.8 4 119248
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 1.08 1.1 92.4 0.864 1.036 0.561 0.503 3 5545
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 2BWI 1.08 42.61 113309 5926 96.93 0.1199 0.1187 0.1186 0.1408 0.1406 RANDOM 14.165
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 34.951 r_sphericity_free 26.423 r_dihedral_angle_4_deg 18.013 r_dihedral_angle_3_deg 11.802 r_sphericity_bonded 7.891 r_dihedral_angle_1_deg 7.869 r_rigid_bond_restr 2.016 r_angle_refined_deg 1.738 r_mcangle_it 1.549 r_mcbond_it 1.238
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.951 r_sphericity_free 26.423 r_dihedral_angle_4_deg 18.013 r_dihedral_angle_3_deg 11.802 r_sphericity_bonded 7.891 r_dihedral_angle_1_deg 7.869 r_rigid_bond_restr 2.016 r_angle_refined_deg 1.738 r_mcangle_it 1.549 r_mcbond_it 1.238 r_mcbond_other 1.192 r_angle_other_deg 1.017 r_chiral_restr 0.115 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2566 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing