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Crystal Structure of PRMT4 with Compound YD1113
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5U4X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.2 M Calcium chloride dihydrate, 0.05 M HEPES sodium pH 7.5, 28% v/v Polyethylene glycol 400, 0.002 M Spermine
Crystal Properties Matthews coefficient Solvent content 3.26 62.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.215 α = 90 b = 84.215 β = 90 c = 130.426 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 EIGER2 X 16M 2022-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
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 1.49 50 100 0.065 0.998 12.6 8.2 87534
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 1.49 1.52 100 0.945 0.75 2 8.1
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 1.49 48.66 85796 1683 99.7 0.17147 0.17134 0.1815 0.17745 0.1875 RANDOM 19.547
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] 0.21 0.11 0.21 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.597 r_dihedral_angle_4_deg 18.723 r_dihedral_angle_3_deg 12.683 r_dihedral_angle_1_deg 6.331 r_long_range_B_refined 5.255 r_long_range_B_other 4.914 r_scangle_other 3.71 r_scbond_it 2.41 r_scbond_other 2.409 r_mcangle_it 2.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.597 r_dihedral_angle_4_deg 18.723 r_dihedral_angle_3_deg 12.683 r_dihedral_angle_1_deg 6.331 r_long_range_B_refined 5.255 r_long_range_B_other 4.914 r_scangle_other 3.71 r_scbond_it 2.41 r_scbond_other 2.409 r_mcangle_it 2.064 r_mcangle_other 2.063 r_angle_refined_deg 1.47 r_angle_other_deg 1.448 r_mcbond_it 1.391 r_mcbond_other 1.391 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 2652 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 50
Software Software Software Name Purpose HKL-3000 data scaling PHASER phasing REFMAC refinement HKL-3000 data reduction