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Co-crystal structure of PERK with compound 24
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 277 100 mM HEPES pH 7.0, 180 mM Na/K tartrate, 9% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.43 64.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.9 α = 90 b = 125.9 β = 90 c = 55.216 γ = 120
Symmetry Space Group P 32 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 PILATUS 6M 2019-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.92 41.51 95.3 0.097 0.997 9.5 6.7 10640
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.92 2.97 0.794 0.817
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 2.92 41.51 10631 509 95.149 0.248 0.246 0.3071 0.2796 0.3171 93.984
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] -8.076 -4.038 -8.076 26.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.157 r_dihedral_angle_4_deg 16.193 r_dihedral_angle_3_deg 15.414 r_lrange_it 8.277 r_lrange_other 8.275 r_dihedral_angle_1_deg 5.771 r_mcangle_it 5.499 r_mcangle_other 5.497 r_scangle_it 4.06 r_scangle_other 4.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.157 r_dihedral_angle_4_deg 16.193 r_dihedral_angle_3_deg 15.414 r_lrange_it 8.277 r_lrange_other 8.275 r_dihedral_angle_1_deg 5.771 r_mcangle_it 5.499 r_mcangle_other 5.497 r_scangle_it 4.06 r_scangle_other 4.059 r_mcbond_it 3.093 r_mcbond_other 3.082 r_scbond_it 2.128 r_scbond_other 2.127 r_angle_refined_deg 1.21 r_angle_other_deg 0.979 r_symmetry_nbd_refined 0.209 r_nbd_other 0.184 r_nbd_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.176 r_symmetry_nbd_other 0.161 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.144 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.035 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2106 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing