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Inter-dimeric interface controls function and stability of S-methionine adenosyltransferase from U. urealiticum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RJS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M Mg Formate and 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.33 47.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.372 α = 90 b = 79.467 β = 105.11 c = 143.787 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-F 2017-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.978 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.55 47.78 99.6 0.076 0.996 5.9 6.8 100906
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 2.55 2.6 0.612 0.64
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 6RJS 2.56 47.78 95107 4982 99.24 0.26136 0.26016 0.2601 0.28409 0.2832 RANDOM 64.964
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] -1.32 3.9 0.57 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.354 r_dihedral_angle_3_deg 18.334 r_dihedral_angle_4_deg 17.248 r_dihedral_angle_1_deg 5.845 r_long_range_B_refined 5.299 r_long_range_B_other 5.298 r_angle_refined_deg 2.215 r_mcangle_it 2.194 r_mcangle_other 2.194 r_scangle_other 2.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.354 r_dihedral_angle_3_deg 18.334 r_dihedral_angle_4_deg 17.248 r_dihedral_angle_1_deg 5.845 r_long_range_B_refined 5.299 r_long_range_B_other 5.298 r_angle_refined_deg 2.215 r_mcangle_it 2.194 r_mcangle_other 2.194 r_scangle_other 2.018 r_mcbond_it 1.306 r_mcbond_other 1.306 r_angle_other_deg 1.202 r_scbond_it 1.19 r_scbond_other 1.19 r_chiral_restr 0.154 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 23398 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 559
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing