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Crystal Structure of phthalate dioxygenase in complex with phthalate
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, calcium chloride, magnesium chloride, sodium potassium tartrate
Crystal Properties Matthews coefficient Solvent content 3.12 60.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.03 α = 90 b = 122.18 β = 101.13 c = 162.94 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 PILATUS 6M 2020-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
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 2.74 159.88 98.1 0.995 12.6 1.9 88962
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 2.74 2.79 0.805
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 2.74 159.88 84574 4388 98.03 0.2104 0.2067 0.2066 0.2826 0.2827 RANDOM 50.688
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] -0.16 -0.03 0.17 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.39 r_dihedral_angle_3_deg 18.315 r_dihedral_angle_4_deg 17.982 r_dihedral_angle_1_deg 8.124 r_angle_refined_deg 1.409 r_chiral_restr 0.109 r_gen_planes_refined 0.006 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19274 Nucleic Acid Atoms Solvent Atoms 1229 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction Aimless data scaling MOLREP phasing