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Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 3
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 6 291 10% PEG 4000, 0.1 M sodium citrate (pH 6.0), 0.2 M magnesium chloride, 1 mM methylthioadenosine
Crystal Properties Matthews coefficient Solvent content 2.79 55.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.49 α = 90 b = 136.41 β = 90 c = 178.02 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 PILATUS 6M 2020-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0000 SPring-8 BL45XU
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 2.75 46.32 100 0.174 0.995 10.1 9.5 32799 56.65
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 2.75 2.9 100 1.052 0.872 2 9.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 2.75 46.32 1.36 32789 1577 99.95 0.2207 0.2185 0.2642 0.2441 61.86
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.2236 f_angle_d 0.5975 f_chiral_restr 0.0451 f_plane_restr 0.0041 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7346 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 142
Software Software Software Name Purpose PHENIX refinement REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing