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Crystal structure of PRMT5:MEP50 in complex with MTA and compound 41
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other A previously determined proprietary structure (which was ultimately derived from PDB entry 8VEO) provided the initial phases.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 10% PEG 4000, 0.1 M sodium citrate (pH 6.0), 0.2 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.81 56.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.65 α = 90 b = 137.84 β = 90 c = 179.09 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 EIGER X 9M 2019-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.07812 APS 21-ID-D
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 2.82 44.8 98.9 0.122 0.126 0.034 0.998 14.2 13.5 30319
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 2.82 2.89 98.4 1.154 1.197 0.317 0.924 14.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS THROUGHOUT 2.82 44.8 28805 1500 98.73 0.23134 0.22868 0.2433 0.28094 0.2925 RANDOM 86.3
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] 14.11 -1.25 -12.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.075 r_dihedral_angle_3_deg 16.563 r_dihedral_angle_4_deg 16.198 r_dihedral_angle_1_deg 7.611 r_mcangle_it 3.375 r_mcangle_other 3.374 r_scangle_other 2.549 r_mcbond_it 1.902 r_mcbond_other 1.902 r_scbond_it 1.385
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.075 r_dihedral_angle_3_deg 16.563 r_dihedral_angle_4_deg 16.198 r_dihedral_angle_1_deg 7.611 r_mcangle_it 3.375 r_mcangle_other 3.374 r_scangle_other 2.549 r_mcbond_it 1.902 r_mcbond_other 1.902 r_scbond_it 1.385 r_scbond_other 1.385 r_angle_refined_deg 1.292 r_angle_other_deg 1.081 r_chiral_restr 0.044 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7391 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction REFMAC phasing