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Human PRMT5 in complex with AZ compound 12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 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 2.85 56.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.249 α = 90 b = 138.648 β = 90 c = 177.727 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 2023-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95373 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.147 109.318 92.6 0.998 8.2 6.9 30022
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.147 2.458 0.728
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 2.15 109.318 28478 1534 43.86 0.26988 0.26938 0.2683 0.27908 0.2792 RANDOM 52.013
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] 0.02 -0.64 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.838 r_dihedral_angle_1_deg 5.634 r_dihedral_angle_2_deg 2.984 r_long_range_B_refined 1.599 r_long_range_B_other 1.598 r_mcangle_it 0.89 r_mcangle_other 0.89 r_angle_refined_deg 0.766 r_scangle_other 0.52 r_mcbond_it 0.474
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.838 r_dihedral_angle_1_deg 5.634 r_dihedral_angle_2_deg 2.984 r_long_range_B_refined 1.599 r_long_range_B_other 1.598 r_mcangle_it 0.89 r_mcangle_other 0.89 r_angle_refined_deg 0.766 r_scangle_other 0.52 r_mcbond_it 0.474 r_mcbond_other 0.474 r_angle_other_deg 0.307 r_scbond_it 0.256 r_scbond_other 0.256 r_chiral_restr 0.038 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 7239 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling MOLREP phasing