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Structure of PYCR1 complexed with the allosteric inhibitor 7-benzamido-4-hydroxynaphthalene-2-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, 13% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 12 mM 7-benzamido-4-hydroxynaphthalene-2-sulfonic acid. Crystal was soaked in cryobuffer containing 20% PEG 200 and 100 mM 7-benzamido-4-hydroxynaphthalene-2-sulfonic acid
Crystal Properties Matthews coefficient Solvent content 2.48 50.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.602 α = 90 b = 179.591 β = 106.49 c = 88.199 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 16M 2025-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97920 APS 24-ID-E
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 1.66 90.7 99.1 0.094 0.102 0.038 0.999 12 6.9 374809
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 1.66 1.69 99 1.303 1.409 0.53 0.55 6.8
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 1.66 61.56 0.08 374809 19156 98.34 0.1843 0.1832 0.1788 0.2034 0.2001
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 11.948 f_angle_d 0.822 f_chiral_restr 0.051 f_plane_restr 0.008 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9706 Nucleic Acid Atoms Solvent Atoms 735 Heterogen Atoms 80
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHENIX phasing