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Co-crystal structure of PERK with inhibitor (R)-2-amino-N-cyclopropyl-5-(4-(2-(3,5-difluorophenyl)-2-hydroxyacetamido)-2-methylphenyl)nicotinamide
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 5.6 293 15% MPD, 10% PEG 8K, 0.1M MgCl2, 0.1M sodium citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.98 58.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.827 α = 90 b = 84.958 β = 90 c = 70.031 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 PILATUS 6M 2019-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.809 56 100 0.118 0.131 0.053 6.5 6.3 11251
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.809 2.88 0.865 0.901 0.35 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4X7J 2.809 55.726 11219 540 99.884 0.234 0.232 0.241 0.2725 0.2891 90.189
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] -14.449 2.416 12.033
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.207 r_dihedral_angle_3_deg 18.519 r_dihedral_angle_4_deg 15.377 r_lrange_it 9.698 r_lrange_other 9.696 r_mcangle_it 7.046 r_mcangle_other 7.046 r_dihedral_angle_1_deg 6.751 r_scangle_it 6.137 r_scangle_other 6.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.207 r_dihedral_angle_3_deg 18.519 r_dihedral_angle_4_deg 15.377 r_lrange_it 9.698 r_lrange_other 9.696 r_mcangle_it 7.046 r_mcangle_other 7.046 r_dihedral_angle_1_deg 6.751 r_scangle_it 6.137 r_scangle_other 6.136 r_mcbond_it 4.263 r_mcbond_other 4.261 r_scbond_other 3.568 r_scbond_it 3.567 r_angle_refined_deg 1.265 r_angle_other_deg 1.117 r_symmetry_nbd_refined 0.199 r_nbd_refined 0.191 r_symmetry_nbd_other 0.168 r_nbtor_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.162 r_nbd_other 0.139 r_xyhbond_nbd_refined 0.133 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.044 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2122 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing