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Crystal Structure of phthalate dioxygenase from Comamonas testosteroni KF1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7FHR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 PEG4000, magnesium chloride, calcium chloride, sodium potassium tartrate
Crystal Properties Matthews coefficient Solvent content 2.91 57.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.248 α = 90 b = 121.375 β = 100.95 c = 161.533 γ = 90
Symmetry Space Group C 1 2 1
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 2M VERTICAL CRL 2020-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.965 ESRF ID30B
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 2.11 158.59 99 0.968 3.9 1.8 191985
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 2.11 2.15 94 0.828
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 7FHR 2.11 158.59 182379 9468 98.9 0.1686 0.166 0.1683 0.2195 0.1683 RANDOM 37.679
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] 0.14 0.03 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.226 r_dihedral_angle_4_deg 18.142 r_dihedral_angle_3_deg 15.683 r_dihedral_angle_1_deg 7.81 r_angle_refined_deg 2.046 r_chiral_restr 0.137 r_gen_planes_refined 0.012 r_bond_refined_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19344 Nucleic Acid Atoms Solvent Atoms 2630 Heterogen Atoms 154
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction xia2 data scaling MOLREP phasing