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PARK7 with covalent inhibitor JYQ-88
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.1 M Ammonium sulfate
0.1 M Bis-Tris pH 5.5
25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.82 56.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.743 α = 90 b = 66.743 β = 90 c = 176.785 γ = 120
Symmetry Space Group P 65 2 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 EIGER2 XE 16M 2020-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97996 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.42 58.93 100 0.033 1 17.5 32.5 44987
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.42 1.44 98.9 1.416 0.335 0.8 9.1
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 6M8Z 1.42 57.802 44848 2289 99.842 0.176 0.1741 0.1746 0.2138 0.2143 31.274
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] 3.024 1.512 3.024 -9.811
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.481 r_dihedral_angle_4_deg 17.535 r_rigid_bond_restr 13.458 r_dihedral_angle_3_deg 13.248 r_dihedral_angle_other_3_deg 12.155 r_scangle_it 7.187 r_scangle_other 7.187 r_lrange_other 6.672 r_lrange_it 6.669 r_dihedral_angle_1_deg 6.405
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.481 r_dihedral_angle_4_deg 17.535 r_rigid_bond_restr 13.458 r_dihedral_angle_3_deg 13.248 r_dihedral_angle_other_3_deg 12.155 r_scangle_it 7.187 r_scangle_other 7.187 r_lrange_other 6.672 r_lrange_it 6.669 r_dihedral_angle_1_deg 6.405 r_scbond_other 5.781 r_scbond_it 5.778 r_mcangle_it 5.413 r_mcangle_other 5.412 r_mcbond_it 4.72 r_mcbond_other 4.717 r_angle_refined_deg 1.985 r_angle_other_deg 1.581 r_symmetry_nbd_refined 0.262 r_nbd_other 0.222 r_nbd_refined 0.209 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.141 r_symmetry_xyhbond_nbd_refined 0.13 r_chiral_restr 0.106 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1375 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing