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Crystal structure of S-adenosylmethionine synthetase from Mycobacterium marinum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IML PDB entry 3IML
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 MymaA.01625.a.A1 PW30103 at 40.19 mg/mL against JCSG+ screen condition E11, 0.16 M calcium acetate, 80 mM sodium cacodylate pH 6.5, 14.4% PEG 8000, 20% glycerol and 25% ethylene glycol as additional cryo-protectant, crystal tracking ID 220762e11, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.61 52.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.6 α = 90 b = 196.23 β = 90 c = 59.66 γ = 90
Symmetry Space Group P 21 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 CCD ADSC QUANTUM 315r 2011-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97740 ALS 5.0.1
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 50 98.3 0.043 29.7 5.8 62515 61471 -3 26.298
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 2.05 84.7 0.168 7.62 4.6 4572
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 PDB entry 3IML 2 50 61296 3101 98.06 0.1566 0.155 0.1632 0.187 0.196 RANDOM 21.4777
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] 1.99 -1.27 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.398 r_dihedral_angle_4_deg 16.686 r_dihedral_angle_3_deg 12.812 r_dihedral_angle_1_deg 5.973 r_scangle_it 3.858 r_scbond_it 2.36 r_angle_refined_deg 1.381 r_mcangle_it 1.239 r_mcbond_it 0.678 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.398 r_dihedral_angle_4_deg 16.686 r_dihedral_angle_3_deg 12.812 r_dihedral_angle_1_deg 5.973 r_scangle_it 3.858 r_scbond_it 2.36 r_angle_refined_deg 1.381 r_mcangle_it 1.239 r_mcbond_it 0.678 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5626 Nucleic Acid Atoms Solvent Atoms 507 Heterogen Atoms 31
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction