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Crystal structure of PRMT5:MEP50 in complex with MTA and TNG462
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 2.67 54.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.21 α = 90 b = 136.6 β = 90 c = 178.01 γ = 90
Symmetry Space Group P 21 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 2022-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03317 APS 23-ID-B
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 2.47 29.7 59.4 0.156 0.998 13.3 13.7 52173 81.22
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 2.47 2.54 2.7 0.778 0.931 3.5 13.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 2.47 29.7 2 52128 2605 59.95 0.2116 0.2099 0.2099 0.2429 0.2432 85.31
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 12.3674 f_angle_d 0.512 f_chiral_restr 0.0441 f_plane_restr 0.0041 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14662 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 127
Software Software Software Name Purpose PHENIX refinement REFMAC refinement XDS data reduction STARANISO data scaling REFMAC phasing