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Crystal structure of human bleomycin hydrolase C73A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7V5L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 30% (w/v) PEG 400, 0.1mM CHES, pH 9.5
Crystal Properties Matthews coefficient Solvent content 12.26 89.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 318.269 α = 90 b = 318.269 β = 90 c = 318.269 γ = 90
Symmetry Space Group I 41 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2021-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 0.9732 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.02 30 100 0.98 14.2 11.3 53491
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.02 3.13 100 0.865 2.7 11.9
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 7V5L 3.02 29.83 50745 2641 99.65 0.1808 0.18 0.1864 0.1972 0.2035 RANDOM 63.93
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 35.396 r_dihedral_angle_4_deg 21.163 r_dihedral_angle_3_deg 18.097 r_dihedral_angle_1_deg 6.857 r_angle_refined_deg 1.664 r_angle_other_deg 1.287 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.396 r_dihedral_angle_4_deg 21.163 r_dihedral_angle_3_deg 18.097 r_dihedral_angle_1_deg 6.857 r_angle_refined_deg 1.664 r_angle_other_deg 1.287 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3684 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 23
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing