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PRMT5 Bound to Compound 8 and MTA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GQB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277.15 11-22% PEG 3350, 200 mM ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.78 55.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.96 α = 90 b = 136.338 β = 90 c = 178.513 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 2022-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 2.0.1 1.03769 ALS 2.0.1
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 3.04 44.27 99.57 0.3068 0.3327 0.1273 0.978 5.7 6.7 24347 76.48
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 3.04 3.18 1.812 1.963 0.7504 0.566 0.94
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 MOLECULAR REPLACEMENT FREE R-VALUE 3.04 44.27 1.33 24230 1178 99.57 0.2176 0.2154 0.2598 0.2391 87.83
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 12.6536 f_angle_d 0.4844 f_chiral_restr 0.0431 f_plane_restr 0.0039 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7337 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 66
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing