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Crystal structure of PRMT3 with compound YD1113
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 8.5 291 0.1 M TRIS hydrochloride pH 8.5, 2.0 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.66 53.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.808 α = 90 b = 99.863 β = 90 c = 170.314 γ = 90
Symmetry Space Group C 2 2 21
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 2022-04-22 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 2.02 50 99.8 0.075 1 9.4 6.3 53430
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 2.02 2.05 100 0.975 0.693 1.9 6.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.02 47.96 52232 1153 99.7 0.19562 0.19485 0.2039 0.23172 0.2394 RANDOM 34.889
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] 1.2 -0.59 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.025 r_dihedral_angle_3_deg 14.435 r_dihedral_angle_4_deg 14.427 r_dihedral_angle_1_deg 7.108 r_long_range_B_refined 5.854 r_long_range_B_other 5.851 r_scangle_other 4.477 r_mcangle_it 3.162 r_mcangle_other 3.162 r_scbond_it 2.961
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.025 r_dihedral_angle_3_deg 14.435 r_dihedral_angle_4_deg 14.427 r_dihedral_angle_1_deg 7.108 r_long_range_B_refined 5.854 r_long_range_B_other 5.851 r_scangle_other 4.477 r_mcangle_it 3.162 r_mcangle_other 3.162 r_scbond_it 2.961 r_scbond_other 2.951 r_mcbond_it 2.302 r_mcbond_other 2.3 r_angle_refined_deg 1.422 r_angle_other_deg 1.279 r_chiral_restr 0.063 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 4840 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 74
Software Software Software Name Purpose HKL-3000 data scaling PHASER phasing REFMAC refinement