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Structure of PYCR1 complexed with the allosteric inhibitor 2-[(2,6-dichlorophenyl)amino]pyridine-3-sulfonic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8TCX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Resevoir contained 400 mM Li2SO4,12% (w/v) PEG 3350, and 0.1 mM HEPES at pH 7.5. Enzyme solution contained 25 mM 2-[(2,6-dichlorophenyl)amino]pyridine-3-sulfonic acid. Crystal was soaked in cryobuffer containing 20% PEG 200 and 50 mM 2-[(2,6-dichlorophenyl)amino]pyridine-3-sulfonic acid.
Crystal Properties Matthews coefficient Solvent content 2.52 51.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.933 α = 90 b = 180.804 β = 106.53 c = 87.945 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 EIGER2 S 9M 2024-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.00002 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.49 47.62 95.8 0.089 0.096 0.036 0.999 15.9 7 508672
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.49 1.52 80.8 2.055 2.238 0.871 0.378 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.49 47.62 0.22 508672 24909 95.03 0.1962 0.195 0.1893 0.2208 0.215
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 f_dihedral_angle_d 11.819 f_angle_d 0.809 f_chiral_restr 0.071 f_plane_restr 0.007 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9752 Nucleic Acid Atoms Solvent Atoms 961 Heterogen Atoms 151
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHENIX phasing