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Human PRMT5:MEP50 in complex with AZD3470
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9EYX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.4 298 14-16 w/v % PEG3350, 24-25 v/v % 2-methyl-2,4-pentanediol and 0.1 M tri-sodium-citrate buffer at pH 5.4
Crystal Properties Matthews coefficient Solvent content 2.91 57.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.29 α = 90 b = 139.369 β = 90 c = 178.549 γ = 90
Symmetry Space Group I 2 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 2022-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95374 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.18 109.863 91.8 0.068 0.028 0.999 14.8 6.8 37249
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.182 2.421 77.4 0.903 0.391 0.707 1.9 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.18 109.86 35344 1885 55.97 0.23577 0.23406 0.2343 0.2684 0.2646 RANDOM 60.046
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] -0.58 -1.43 2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.638 r_dihedral_angle_1_deg 5.6 r_dihedral_angle_2_deg 2.315 r_long_range_B_refined 1.862 r_long_range_B_other 1.86 r_mcangle_it 0.952 r_mcangle_other 0.952 r_angle_refined_deg 0.712 r_scangle_other 0.604 r_mcbond_it 0.511
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.638 r_dihedral_angle_1_deg 5.6 r_dihedral_angle_2_deg 2.315 r_long_range_B_refined 1.862 r_long_range_B_other 1.86 r_mcangle_it 0.952 r_mcangle_other 0.952 r_angle_refined_deg 0.712 r_scangle_other 0.604 r_mcbond_it 0.511 r_mcbond_other 0.511 r_scbond_it 0.317 r_scbond_other 0.315 r_angle_other_deg 0.292 r_chiral_restr 0.035 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7248 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction STARANISO data scaling AMoRE phasing