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PARK7 with inhibitor 8RK64
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 9 293 0.1 M Bicine pH 9.0
10% (w/v) PEG 20 000
2% (w/v) 1,4-dioxane
Crystal Properties Matthews coefficient Solvent content 2.88 57.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.859 α = 90 b = 66.859 β = 90 c = 179.688 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 PILATUS 6M 2019-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96871 Diamond I24
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 1.21 59.9 100 0.028 0.999 16.1 18.1 73359
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 1.21 1.23 100 0.969 0.447 9.6
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 1.21 57.902 73189 3631 99.934 0.133 0.1324 0.1324 0.1547 0.155 19.332
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] -0.35 -0.175 -0.35 1.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.292 r_dihedral_angle_4_deg 18.675 r_dihedral_angle_other_3_deg 14.049 r_dihedral_angle_3_deg 12.542 r_scangle_other 8.193 r_scangle_it 8.149 r_scbond_other 7.338 r_scbond_it 7.299 r_rigid_bond_restr 6.794 r_lrange_other 6.415
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.292 r_dihedral_angle_4_deg 18.675 r_dihedral_angle_other_3_deg 14.049 r_dihedral_angle_3_deg 12.542 r_scangle_other 8.193 r_scangle_it 8.149 r_scbond_other 7.338 r_scbond_it 7.299 r_rigid_bond_restr 6.794 r_lrange_other 6.415 r_dihedral_angle_1_deg 6.311 r_lrange_it 6.122 r_mcangle_it 4.316 r_mcangle_other 4.291 r_mcbond_it 3.378 r_mcbond_other 3.231 r_angle_refined_deg 1.933 r_angle_other_deg 1.612 r_symmetry_xyhbond_nbd_refined 0.529 r_symmetry_nbd_refined 0.234 r_nbd_refined 0.221 r_symmetry_nbd_other 0.171 r_nbtor_refined 0.168 r_nbd_other 0.163 r_chiral_restr 0.122 r_xyhbond_nbd_refined 0.12 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_symmetry_xyhbond_nbd_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1384 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing