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PYCR1 in complex with 1-(2,4-Difluorophenyl)-2-(1H-1,2,4-triazol-1- yl)ethanone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291.15 Based on Morpheus 2.34 condition (Molecular Dimensions) ), containing 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M sodium citrate tribasic, 0.02 M potassium sodium tartrate, 0.02 M sodium oxamate, 0.1 M Tris (base), BICINE pH 8.5, 20% ethylene glycol, 10% PEG 8000, and supplemented with 10% ethylene glycol for cryoprotection.
Crystal Properties Matthews coefficient Solvent content 2.92 57.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.78 α = 90 b = 88.001 β = 90 c = 116.812 γ = 90
Symmetry Space Group P 21 21 2
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 2023-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9763 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.57 38.64 100 0.06 0.06 1 20.46 13.6 234708 27.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.57 1.67 2.03 2.11 0.76 1.41
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.57 38.64 1.35 234475 1998 99.89 0.185 0.1848 0.1849 0.2052 0.2051 44.7
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 11.37 f_angle_d 0.8221 f_chiral_restr 0.0524 f_plane_restr 0.0078 f_bond_d 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10025 Nucleic Acid Atoms Solvent Atoms 842 Heterogen Atoms 154
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling REFMAC phasing