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Crystal Structure of cis-4,5-dihydrodiol phthalate dehydrogenase from Comamonas testosteroni KF1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MOI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% PEG 3350, 0.2 M Ammonium phosphate dibasic, 100 mM Tris buffer pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.49 50.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.177 α = 90 b = 90.696 β = 90 c = 164.11 γ = 90
Symmetry Space Group P 21 21 21
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 2020-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.965460 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 2.8 60.92 95.5 0.943 6.2 1.8 19666
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 2.8 2.95 0.832 3.1
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 3MOI 2.8 60.92 18701 965 95.22 0.1944 0.1909 0.1909 0.2618 0.2617 RANDOM 20.439
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] -0.22 0.1 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.913 r_dihedral_angle_3_deg 19.674 r_dihedral_angle_4_deg 18.419 r_dihedral_angle_1_deg 7.762 r_angle_refined_deg 1.623 r_chiral_restr 0.129 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5351 Nucleic Acid Atoms Solvent Atoms 483 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction Aimless data scaling MOLREP phasing