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Crystal structure of mouse protein arginine methyltransferase 7 in complex with SGC8158 chemical probe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C4A PDB entry 4C4A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 293 20% PEG3350, 0.04 M citric acid, 0.06 M Bis-Tris propane, pH 6.4
Crystal Properties Matthews coefficient Solvent content 2.59 52.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.813 α = 90 b = 97.813 β = 90 c = 169.539 γ = 90
Symmetry Space Group P 43 21 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 16M 2019-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
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 2.4 50 99.7 0.114 0.118 0.033 9.5 12.9 33363
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 2.4 2.44 100 1.172 1.223 0.346 0.689 12.2
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 PDB entry 4C4A 2.4 47.03 31243 1632 99.74 0.2111 0.20849 0.214 0.26122 0.2659 RANDOM 63.365
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] -0.8 -0.8 1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.786 r_dihedral_angle_4_deg 20.838 r_dihedral_angle_3_deg 15.798 r_long_range_B_other 10.514 r_long_range_B_refined 10.509 r_mcangle_it 8.273 r_mcangle_other 8.272 r_dihedral_angle_1_deg 8.027 r_scangle_other 7.937 r_mcbond_it 5.961
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.786 r_dihedral_angle_4_deg 20.838 r_dihedral_angle_3_deg 15.798 r_long_range_B_other 10.514 r_long_range_B_refined 10.509 r_mcangle_it 8.273 r_mcangle_other 8.272 r_dihedral_angle_1_deg 8.027 r_scangle_other 7.937 r_mcbond_it 5.961 r_mcbond_other 5.96 r_scbond_other 5.847 r_scbond_it 5.844 r_angle_refined_deg 1.365 r_angle_other_deg 1.18 r_chiral_restr 0.055 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 4702 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-3000 data reduction