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Co-crystal structure of compound 3S bound to the Catalytic domain of human PAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HYC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277.15 0.1 M Hepes pH7.0, 10% EG, 20% PEG2000
Crystal Properties Matthews coefficient Solvent content 2.99 58.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.84 α = 90 b = 107.48 β = 90 c = 123.8 γ = 90
Symmetry Space Group C 2 2 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 6M 2018-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.0332 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.92 49.34 100 0.045 0.019 21.1 6.6 33903
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 1.92 9.01 0.9
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 1.92 49.34 32198 1678 99.88 0.18034 0.17814 0.1895 0.21996 0.2248 RANDOM 42.029
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] -1.33 4.1 -2.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.844 r_long_range_B_refined 8.727 r_long_range_B_other 8.717 r_scangle_other 7.06 r_dihedral_angle_1_deg 6.798 r_mcangle_other 5.088 r_mcangle_it 5.087 r_scbond_it 4.788 r_scbond_other 4.788 r_dihedral_angle_2_deg 3.851
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.844 r_long_range_B_refined 8.727 r_long_range_B_other 8.717 r_scangle_other 7.06 r_dihedral_angle_1_deg 6.798 r_mcangle_other 5.088 r_mcangle_it 5.087 r_scbond_it 4.788 r_scbond_other 4.788 r_dihedral_angle_2_deg 3.851 r_mcbond_it 3.817 r_mcbond_other 3.794 r_angle_refined_deg 1.663 r_angle_other_deg 0.564 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 2532 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PDB_EXTRACT data extraction REFMAC phasing