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Human PRMT5:MEP50 structure with Fragment (Example 18) and MTA Bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EML
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 15% PEG3350, 100 mM Na citrate, pH 5.4, 100mM Carboxylic acids
Crystal Properties Matthews coefficient Solvent content 2.9 57.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.282 α = 90 b = 138.654 β = 90 c = 178.871 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 EIGER2 XE 16M 2021-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9197 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.97 109.59 93.25 0.99 10.7 11.9 39692 1.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.26 90.9 0.77
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 5EML 2.01 109.59 37769 1957 46.23 0.2214 0.2188 0.2231 0.2708 0.2702 RANDOM 30.724
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] 5.52 -2.53 -2.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.036 r_dihedral_angle_4_deg 21.098 r_dihedral_angle_3_deg 19.08 r_dihedral_angle_1_deg 8.533 r_mcangle_it 2.387 r_angle_other_deg 2.356 r_angle_refined_deg 1.52 r_mcbond_it 1.348 r_mcbond_other 1.348 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.036 r_dihedral_angle_4_deg 21.098 r_dihedral_angle_3_deg 19.08 r_dihedral_angle_1_deg 8.533 r_mcangle_it 2.387 r_angle_other_deg 2.356 r_angle_refined_deg 1.52 r_mcbond_it 1.348 r_mcbond_other 1.348 r_chiral_restr 0.064 r_bond_other_d 0.035 r_gen_planes_other 0.008 r_bond_refined_d 0.007 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7399 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling REFMAC phasing