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Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 24
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 2.76 55.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.56 α = 90 b = 137.732 β = 90 c = 177.676 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 2019-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0000 SPring-8 BL45XU
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 2.69 45.65 100 0.15 0.156 0.042 0.999 15.1 13.5 34631
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 2.69 2.82 99.9 1.326 1.38 0.378 0.902 13.1
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 2.69 45.65 32905 1723 99.94 0.22293 0.22042 0.2348 0.26949 0.2804 RANDOM 70.332
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] 11.69 -2.61 -9.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.621 r_dihedral_angle_4_deg 19.222 r_dihedral_angle_3_deg 16.724 r_long_range_B_refined 9.013 r_long_range_B_other 9.013 r_dihedral_angle_1_deg 7.749 r_mcangle_it 6.75 r_mcangle_other 6.75 r_scangle_other 5.578 r_mcbond_it 4.213
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.621 r_dihedral_angle_4_deg 19.222 r_dihedral_angle_3_deg 16.724 r_long_range_B_refined 9.013 r_long_range_B_other 9.013 r_dihedral_angle_1_deg 7.749 r_mcangle_it 6.75 r_mcangle_other 6.75 r_scangle_other 5.578 r_mcbond_it 4.213 r_mcbond_other 4.212 r_scbond_it 3.391 r_scbond_other 3.391 r_angle_refined_deg 1.385 r_angle_other_deg 1.112 r_chiral_restr 0.049 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 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 7346 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction