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PRMT5(M420T mutant):MEP50 complexed with inhibitor PF-06855800
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7MXA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 286 Crystallization of full-length human PRMT5/MEP50 complexed with cofactor site inhibitors was performed at 13 degrees Celsius by hanging-drop vapor-diffusion methods. 2.5 ul of a solution of 5:1 molar ratio of inhibitor compound to PRMT5/MEP50 complex (13 mg/mL) was mixed with 2.5 ul of reservoir solution containing 13-15% (w/v) PEG3350, 0.1M MES, pH 6.5-7.5, 0.25M NaCl, and 20% (v/v) ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 2.92 57.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.407 α = 90 b = 138.451 β = 90 c = 178.452 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 95 PIXEL DECTRIS PILATUS 6M 2017-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.39 109.39 99.8 0.082 0.042 12.5 6.5 96383
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.39 2.52 0.69 0.284
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 7MXA 2.395 109.39 96296 4716 99.8 0.2297 0.2269 0.2236 0.282 0.2794 RANDOM 59.01
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] -28.6806 1.9717 26.7089
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.12 t_omega_torsion 3.5 t_angle_deg 1 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14652 Nucleic Acid Atoms Solvent Atoms 805 Heterogen Atoms 54
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing