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Co-crystal Structure of PERK bound to 4-[2-amino-4-methyl-3-(2-methylquinolin-6-yl)benzoyl]-1-methyl-2,5-diphenyl-1,2-dihydro-3H-pyrazol-3-one inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X7J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 0.4M Na/K Tartrate, 0.1M HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.91 57.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.576 α = 90 b = 81.576 β = 90 c = 128.84 γ = 90
Symmetry Space Group P 41 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 IMAGE PLATE RIGAKU RAXIS IV++ 2011-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.35 50 98.6 0.13 5.9 4.7 18581
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.43 92.7 0.604 3.8 1706
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4X7J 2.35 40.79 961 98.08 0.211 0.2092 0.2454 0.208 RANDOM 28.947
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] 0.29 0.29 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.949 r_dihedral_angle_4_deg 16.51 r_dihedral_angle_3_deg 12.393 r_dihedral_angle_1_deg 4.667 r_scangle_it 1.575 r_angle_refined_deg 1.062 r_scbond_it 0.948 r_mcangle_it 0.638 r_mcbond_it 0.328 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.949 r_dihedral_angle_4_deg 16.51 r_dihedral_angle_3_deg 12.393 r_dihedral_angle_1_deg 4.667 r_scangle_it 1.575 r_angle_refined_deg 1.062 r_scbond_it 0.948 r_mcangle_it 0.638 r_mcbond_it 0.328 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2122 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 50
Software Software Software Name Purpose HKL-2000 data reduction REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling REFMAC phasing