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Crystal structure of PRMT5:MEP50 in complex with MTA and compound 51
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8VEO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 10% PEG 4000, 0.1 M sodium citrate (pH 6.0), 0.2 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.84 56.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.946 α = 90 b = 137.889 β = 90 c = 178.607 γ = 90
Symmetry Space Group I 2 2 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 S 9M 2024-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.07 109.15 93.5 0.16 0.045 0.998 12.9 13.5 36863
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.365 81.5 1.343 0.42 0.758 1.9 11.1
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 2.07 109.15 35038 1825 47.64 0.2241 0.22165 0.27273 0.2432 RANDOM 42.548
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] 0.46 -0.38 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.888 r_dihedral_angle_1_deg 7.25 r_dihedral_angle_2_deg 5.608 r_long_range_B_refined 4.455 r_long_range_B_other 4.454 r_mcangle_it 2.467 r_mcangle_other 2.467 r_scangle_other 1.845 r_mcbond_it 1.37 r_mcbond_other 1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.888 r_dihedral_angle_1_deg 7.25 r_dihedral_angle_2_deg 5.608 r_long_range_B_refined 4.455 r_long_range_B_other 4.454 r_mcangle_it 2.467 r_mcangle_other 2.467 r_scangle_other 1.845 r_mcbond_it 1.37 r_mcbond_other 1.37 r_angle_refined_deg 1.005 r_scbond_it 0.995 r_scbond_other 0.995 r_angle_other_deg 0.356 r_chiral_restr 0.045 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7313 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 125
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling REFMAC phasing