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Crystal structure of Human PRMT6 in complex with S-Adenosyl-L-Homocysteine and YS17-117 Compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EGS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M Sodium Malonate pH 7.0, 12% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.58 52.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.091 α = 90 b = 135.133 β = 98.01 c = 83.206 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN A200 2019-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 50 99.9 0.093 0.101 0.038 9.8 7 114589
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 2.03 98 0.927 1.016 0.409 0.718 5.9
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 FOURIER SYNTHESIS THROUGHOUT 5EGS 2 32.5 111464 2659 99.17 0.1851 0.1842 0.1936 0.2217 0.2265 RANDOM 35.12
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] -0.38 1.1 -0.63 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.036 r_dihedral_angle_4_deg 16.702 r_dihedral_angle_3_deg 13.32 r_dihedral_angle_1_deg 6.035 r_angle_refined_deg 1.422 r_angle_other_deg 0.927 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.036 r_dihedral_angle_4_deg 16.702 r_dihedral_angle_3_deg 13.32 r_dihedral_angle_1_deg 6.035 r_angle_refined_deg 1.422 r_angle_other_deg 0.927 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10574 Nucleic Acid Atoms Solvent Atoms 767 Heterogen Atoms 200
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing HKL-3000 data reduction HKL-3000 data collection