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Structure of PYCR1 complexed with 2-chloro-5-(2-oxoimidazolidin-1-yl)benzoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XP3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Reservoir contained 350 mM Li2SO4, 20% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 16 mM 2-chloro-5-(2-oxoimidazolidin-1-yl)benzoic acid. Crystal was soaked in cryobuffer containing 0 mM Li2SO4, 20% PEG 200, and 25 mM 2-chloro-5-(2-oxoimidazolidin-1-yl)benzoic acid
Crystal Properties Matthews coefficient Solvent content 2.41 48.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.009 α = 90 b = 178.914 β = 107.12 c = 88.078 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 EIGER X 16M 2023-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
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 2 89.46 95.6 0.127 0.166 0.106 0.983 9.4 2.2 103502
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 2 2.03 95.2 0.768 1.003 0.638 0.412 2.2
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 2 89.46 1.37 103471 5204 95.45 0.1905 0.189 0.1887 0.2193 0.2188
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 12.916 f_angle_d 0.889 f_chiral_restr 0.049 f_plane_restr 0.008 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9868 Nucleic Acid Atoms Solvent Atoms 397 Heterogen Atoms 105
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHENIX phasing