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Crystal structure of PRMT5:MEP50 in complex with MTA and compound 46a
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 291 10% PEG 4000, 0.1 M sodium citrate (pH 6.0), 0.2 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.73 54.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.14 α = 90 b = 137.69 β = 90 c = 178.43 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 PILATUS3 6M 2019-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97853 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.67 45.1 99.9 0.085 0.093 0.036 0.999 14.9 6.7 35013
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.67 2.8 99.9 0.707 0.77 0.302 0.934 6.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.67 37.44 1.35 34913 1722 99.67 0.2226 0.22 0.2199 0.2708 0.2704 RANDOM 80.02
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 14.6284 f_angle_d 1.6749 f_chiral_restr 0.0898 f_bond_d 0.0135 f_plane_restr 0.0032
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7315 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 132
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction REFMAC phasing