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Crystal Structure of PRMT3 with Compound YD1-214
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 7 291 2.4 M Sodium malonate pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.82 56.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.211 α = 90 b = 70.211 β = 90 c = 175.142 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 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 1.92 50 100 0.063 1 9.7 18.1 34468
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 1.92 1.95 100 0.985 0.894 2.5 17.6
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 1.92 49.7 33334 1058 99.95 0.18561 0.18466 0.1928 0.21491 0.2333 RANDOM 36.116
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] 0.5 0.5 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.883 r_dihedral_angle_3_deg 14.045 r_dihedral_angle_4_deg 11.752 r_dihedral_angle_1_deg 7.214 r_long_range_B_refined 7.009 r_long_range_B_other 6.984 r_scangle_other 5.415 r_mcangle_it 4.083 r_mcangle_other 4.081 r_scbond_other 3.529
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.883 r_dihedral_angle_3_deg 14.045 r_dihedral_angle_4_deg 11.752 r_dihedral_angle_1_deg 7.214 r_long_range_B_refined 7.009 r_long_range_B_other 6.984 r_scangle_other 5.415 r_mcangle_it 4.083 r_mcangle_other 4.081 r_scbond_other 3.529 r_scbond_it 3.527 r_mcbond_it 3 r_mcbond_other 2.994 r_angle_refined_deg 1.335 r_angle_other_deg 1.314 r_chiral_restr 0.064 r_bond_refined_d 0.009 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 2391 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 31
Software Software Software Name Purpose HKL-3000 data scaling HKL-3000 data reduction PHASER phasing REFMAC refinement