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Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 28
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 291 10% PEG 4000, 0.2M magnesium chloride, 0.1M sodium citrate (pH 6.0)
Crystal Properties Matthews coefficient Solvent content 2.7 54.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.47 α = 90 b = 136.35 β = 90 c = 177.69 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 PILATUS3 6M 2019-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97930 SSRF BL18U1
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 2.79 45.2 99.9 0.087 0.095 0.037 0.999 15.1 6.6 30399
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 2.79 2.94 99.8 0.763 0.829 0.32 0.945 6.6
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 2.79 45.2 28776 1497 99.41 0.22861 0.22641 0.2345 0.26972 0.2757 RANDOM 88.96
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] 7.01 -0.8 -6.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.901 r_dihedral_angle_4_deg 18.516 r_dihedral_angle_3_deg 16.581 r_dihedral_angle_1_deg 7.713 r_long_range_B_refined 4.533 r_long_range_B_other 4.532 r_mcangle_it 2.215 r_mcangle_other 2.215 r_scangle_other 1.982 r_angle_refined_deg 1.437
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.901 r_dihedral_angle_4_deg 18.516 r_dihedral_angle_3_deg 16.581 r_dihedral_angle_1_deg 7.713 r_long_range_B_refined 4.533 r_long_range_B_other 4.532 r_mcangle_it 2.215 r_mcangle_other 2.215 r_scangle_other 1.982 r_angle_refined_deg 1.437 r_mcbond_it 1.293 r_mcbond_other 1.293 r_scbond_it 1.144 r_scbond_other 1.144 r_angle_other_deg 1.126 r_chiral_restr 0.051 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7338 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction