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Crystal Structure of PRMT4 with Compound YD1290
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 9 291 0.1 M BICINE pH 9.0, 2.0 M Magnesium chloride hexahydrate
Crystal Properties Matthews coefficient Solvent content 3.63 66.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.659 α = 90 b = 86.659 β = 90 c = 137.066 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 2022-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
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 2.17 50 99.6 0.069 1 7.2 16.4 32051
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 2.17 2.21 99.2 0.991 0.851 2 13.2
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 2.17 45.73 30483 1521 99.46 0.20177 0.20064 0.2076 0.22466 0.2287 RANDOM 45.094
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] 0.29 0.14 0.29 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.775 r_dihedral_angle_3_deg 15.016 r_dihedral_angle_4_deg 14.759 r_long_range_B_other 10.396 r_long_range_B_refined 10.391 r_scangle_other 8.749 r_dihedral_angle_1_deg 7.807 r_scbond_it 6.445 r_scbond_other 6.443 r_mcangle_it 6.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.775 r_dihedral_angle_3_deg 15.016 r_dihedral_angle_4_deg 14.759 r_long_range_B_other 10.396 r_long_range_B_refined 10.391 r_scangle_other 8.749 r_dihedral_angle_1_deg 7.807 r_scbond_it 6.445 r_scbond_other 6.443 r_mcangle_it 6.118 r_mcangle_other 6.116 r_mcbond_it 4.801 r_mcbond_other 4.771 r_angle_refined_deg 2.006 r_angle_other_deg 1.468 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 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 2574 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 48
Software Software Software Name Purpose HKL-3000 data scaling PHASER phasing REFMAC refinement