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Copper oxidase from Colletotrichum graminicola
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C86
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 PEG 2K MME, ammonium sulphate, Na acetate
Crystal Properties Matthews coefficient Solvent content 2.75 55.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.111 α = 90 b = 172.111 β = 90 c = 172.111 γ = 90
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 EIGER X 16M 2018-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97951 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.3 70.26 100 0.023 19.2 24.4 37678
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 100 0.216 24.8
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 5C86 2.3 60.92 35829 1819 99.99 0.2408 0.2384 0.2402 0.2862 0.2856 RANDOM 50.291
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 35.949 r_dihedral_angle_3_deg 17.548 r_dihedral_angle_4_deg 16.534 r_dihedral_angle_1_deg 8.675 r_angle_refined_deg 1.769 r_angle_other_deg 1.293 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.949 r_dihedral_angle_3_deg 17.548 r_dihedral_angle_4_deg 16.534 r_dihedral_angle_1_deg 8.675 r_angle_refined_deg 1.769 r_angle_other_deg 1.293 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4505 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing