☰ Navigation Tabs
PRMT5 Bound to Compound 6 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 2.85 56.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.607 α = 90 b = 138.003 β = 90 c = 177.955 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 2022-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 2.0.1 1.03580 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 2.47 44.77 99.61 0.1769 0.192 0.07378 0.994 8.28 6.7 46007 54.7
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 2.47 2.52 2.362 2.564 0.989 0.503 0.74
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.47 44.77 1.34 45868 2221 99.61 0.2262 0.2239 0.232 0.2694 0.2739 73.52
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 17.3283 f_angle_d 0.5383 f_chiral_restr 0.0441 f_plane_restr 0.005 f_bond_d 0.0024
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7327 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 57
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing