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Preserving metallic sites affected by radiation damage: the CuT2 case in Thermus thermophilus multicopper oxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YAE PDB ENTRY 2YAE
Crystallization Crystal Properties Matthews coefficient Solvent content 2.56 51.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.744 α = 90 b = 110.332 β = 90 c = 96.484 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 287 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A NSLS X6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.6 19.72 98.1 0.05 2.5 64734 2 10.58
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 96
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2YAE 1.69 19.687 1.36 54990 2728 98.4 0.1409 0.139 0.1789 0.1629
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 f_dihedral_angle_d 15.894 f_angle_d 1.584 f_chiral_restr 0.112 f_bond_d 0.018 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3439 Nucleic Acid Atoms Solvent Atoms 563 Heterogen Atoms 92
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling REFMAC phasing