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Crystal Structure of PRMT3 with Compound YD1-208
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FYT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 20% PEG3350, 0.3 M Sodium formate
Crystal Properties Matthews coefficient Solvent content 2.77 55.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.14 α = 90 b = 70.14 β = 90 c = 172.37 γ = 90
Symmetry Space Group P 43 21 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 EIGER X 16M 2021-02-13 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 2.08 50 95 0.13 0.136 0.037 0.992 6.1 14.4 25025
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 2.08 2.12 95.7 0.949 0.983 0.248 0.806 14.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.09 49.65 24023 979 94.7 0.20652 0.20525 0.23776 0.235 RANDOM 39.853
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] -0.88 -0.88 1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.577 r_dihedral_angle_4_deg 22.145 r_dihedral_angle_3_deg 14.296 r_dihedral_angle_1_deg 7.381 r_long_range_B_other 5.824 r_long_range_B_refined 5.823 r_scangle_other 4.615 r_mcangle_other 3.806 r_mcangle_it 3.805 r_scbond_it 3.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.577 r_dihedral_angle_4_deg 22.145 r_dihedral_angle_3_deg 14.296 r_dihedral_angle_1_deg 7.381 r_long_range_B_other 5.824 r_long_range_B_refined 5.823 r_scangle_other 4.615 r_mcangle_other 3.806 r_mcangle_it 3.805 r_scbond_it 3.127 r_scbond_other 3.125 r_mcbond_it 2.759 r_mcbond_other 2.749 r_angle_refined_deg 1.439 r_angle_other_deg 1.281 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 2344 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PHASER phasing HKL-3000 data reduction