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Crystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 2 (AtMAT2) in complex with S-adenosylmethionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VCZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 0.12 M Alcohols (1,6-hexanediol; 1-butanol; 1,2-propanediol; 2-propanol; 1,4-butanediol; 1,3-propanediol), 0.1 M HEPES and MOPS buffer at pH 7.5, 20% mmPEG500, 10% PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.97 58.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.98 α = 90 b = 101.354 β = 99.8 c = 84.708 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 EIGER X 16M 2018-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
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 1.97 45.72 97.7 0.063 10.7 3.21 71629 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.09 97.4 0.45 2.6 3.33
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 6VCZ 1.97 45.72 70546 1075 97.76 0.1919 0.1912 0.2078 0.2401 0.2587 RANDOM 35.771
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] 5.86 1.33 -3.06 -3.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.616 r_dihedral_angle_3_deg 15.925 r_dihedral_angle_4_deg 13.361 r_dihedral_angle_1_deg 7.672 r_angle_refined_deg 1.955 r_angle_other_deg 1.399 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.616 r_dihedral_angle_3_deg 15.925 r_dihedral_angle_4_deg 13.361 r_dihedral_angle_1_deg 7.672 r_angle_refined_deg 1.955 r_angle_other_deg 1.399 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6080 Nucleic Acid Atoms Solvent Atoms 616 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing