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Crystal Structure of PRMT4 with Compound YD1-289
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, SITTING DROP 7 291 3.5 M Ammonium chloride, 0.1 M BIS-TRIS propane pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.59 65.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.582 α = 90 b = 86.582 β = 90 c = 136.026 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 EIGER X 16M 2022-10-15 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) Rrim I (All) 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 2.35 50 99.9 0.054 0.057 0.02 0.998 10.3 8.2 25134
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 100 0.987 1.055 0.367 0.702 8.2
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 2.35 45.38 24580 519 99.86 0.19723 0.19613 0.1993 0.24587 0.245 RANDOM 54.216
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] 0.53 0.27 0.53 -1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.892 r_dihedral_angle_4_deg 17.924 r_dihedral_angle_3_deg 15.649 r_long_range_B_other 9.836 r_long_range_B_refined 9.83 r_scangle_other 7.872 r_dihedral_angle_1_deg 7.651 r_mcangle_it 6.289 r_mcangle_other 6.288 r_scbond_other 5.652
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.892 r_dihedral_angle_4_deg 17.924 r_dihedral_angle_3_deg 15.649 r_long_range_B_other 9.836 r_long_range_B_refined 9.83 r_scangle_other 7.872 r_dihedral_angle_1_deg 7.651 r_mcangle_it 6.289 r_mcangle_other 6.288 r_scbond_other 5.652 r_scbond_it 5.651 r_mcbond_it 4.666 r_mcbond_other 4.659 r_angle_refined_deg 1.441 r_angle_other_deg 1.259 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 2604 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PHASER phasing HKL-3000 data reduction