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Crystal Structure of isophthalate dioxygenase from Comamonas testosteroni KF1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% PEG3350, 0.2 M potassium thiocyanate, 0.1 M tris-HCl pH 7.0
Crystal Properties Matthews coefficient Solvent content 5.68 78.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.74 α = 90 b = 150.74 β = 90 c = 150.74 γ = 90
Symmetry Space Group P 21 3
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 2021-09-07 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 2.96 106.82 100 0.997 15 1.9 23991
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 2.96 3.14 0.809 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.96 106.82 22785 1206 99.99 0.1764 0.17484 0.1803 0.20571 0.2067 RANDOM 77.384
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_3_deg 19.067 r_long_range_B_other 12.048 r_long_range_B_refined 12.044 r_scangle_other 11.034 r_dihedral_angle_2_deg 9.763 r_dihedral_angle_1_deg 8.346 r_mcangle_it 8.027 r_mcangle_other 8.026 r_scbond_other 7.913 r_scbond_it 7.904
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.067 r_long_range_B_other 12.048 r_long_range_B_refined 12.044 r_scangle_other 11.034 r_dihedral_angle_2_deg 9.763 r_dihedral_angle_1_deg 8.346 r_mcangle_it 8.027 r_mcangle_other 8.026 r_scbond_other 7.913 r_scbond_it 7.904 r_mcbond_it 5.935 r_mcbond_other 5.91 r_angle_refined_deg 2.034 r_angle_other_deg 0.675 r_chiral_restr 0.092 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3514 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling MOLREP phasing