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Crystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 2 (AtMAT2) in complex with free Methionine and AMPCPP
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 2.91 57.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.941 α = 90 b = 84.721 β = 95.67 c = 119.503 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 RAYONIX MX300-HS 2018-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.000 APS 22-BM
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 39.83 99.8 0.116 8.78 3.21 136621 -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 2 2.07 99.1 0.375 2.13 2.41
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 2 39.83 133001 2672 98.56 0.2226 0.222 0.2292 0.2507 0.2573 RANDOM 26.208
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] 0.05 0.09 0.08 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.743 r_dihedral_angle_3_deg 14.52 r_dihedral_angle_4_deg 13.376 r_dihedral_angle_1_deg 7.168 r_angle_refined_deg 1.66 r_angle_other_deg 1.353 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.743 r_dihedral_angle_3_deg 14.52 r_dihedral_angle_4_deg 13.376 r_dihedral_angle_1_deg 7.168 r_angle_refined_deg 1.66 r_angle_other_deg 1.353 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12053 Nucleic Acid Atoms Solvent Atoms 1201 Heterogen Atoms 252
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction PHASER phasing HKL-3000 data reduction SCALEPACK data scaling