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Green-type copper-nitrite reductase from Sinorhizobium meliloti 2011
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AQ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.2 M MgCl2, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.17 61.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.43 α = 90 b = 215.39 β = 90 c = 114.48 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 PIXEL DECTRIS PILATUS 6M-F 2017-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.928190 Diamond I04-1
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 2.5 78.58 98.9 0.127 0.139 0.057 0.985 9.4 5.7 52802
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 2.5 2.58 97.3 0.86 0.963 0.424 0.675 4.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1AQ8 2.5 78.58 50185 2587 98.6 0.1839 0.1817 0.2243 0.2197 RANDOM 38.279
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] -0.07 -0.03 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.774 r_dihedral_angle_4_deg 22.105 r_dihedral_angle_3_deg 14.821 r_dihedral_angle_1_deg 8.14 r_angle_refined_deg 1.485 r_angle_other_deg 1.135 r_chiral_restr 0.055 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.774 r_dihedral_angle_4_deg 22.105 r_dihedral_angle_3_deg 14.821 r_dihedral_angle_1_deg 8.14 r_angle_refined_deg 1.485 r_angle_other_deg 1.135 r_chiral_restr 0.055 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7511 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 6
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing