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The crystal structure of the yeast arginine methyltransferase SFM1 complexed with MTA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C77
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.2 M NaCl, 0.1 M Tris-HCl (pH 8.5), 38% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.7 27.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.527 α = 90 b = 57.77 β = 106.46 c = 43.153 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 PIXEL DECTRIS PILATUS 6M 2016-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.979 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.7 50 95.4 0.1 11.5 2.6 5087
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 88.1 0.314 0.816 1.9 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 MOLECULAR REPLACEMENT THROUGHOUT 5C77 2.7 50 4608 234 95.07 0.23216 0.22955 0.231 0.28217 0.2818 RANDOM 57.406
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] -4.27 -0.85 7.41 -2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.501 r_dihedral_angle_3_deg 13.702 r_dihedral_angle_4_deg 12.579 r_long_range_B_refined 7.256 r_long_range_B_other 7.254 r_scangle_other 5.642 r_dihedral_angle_1_deg 5.575 r_mcangle_it 4.781 r_mcangle_other 4.779 r_scbond_it 3.764
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.501 r_dihedral_angle_3_deg 13.702 r_dihedral_angle_4_deg 12.579 r_long_range_B_refined 7.256 r_long_range_B_other 7.254 r_scangle_other 5.642 r_dihedral_angle_1_deg 5.575 r_mcangle_it 4.781 r_mcangle_other 4.779 r_scbond_it 3.764 r_scbond_other 3.761 r_mcbond_it 3.23 r_mcbond_other 3.215 r_angle_refined_deg 1.435 r_angle_other_deg 0.967 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_bond_other_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 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 1487 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing