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Crystal structure of a malate synthase G from Mycobacterium marinum bound to acetyl CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S9Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 MymaA.18344.a.B1.PS38275 at 23.7 mg/mL with 2 mM acetyl coenzyme A against JCSG+ screen condition H10 0.2 M ammonium acetate, 0.1 M BisTris pH 5.5, 25% PEG 3350 supplemented with 15% EG as cryo-protectant, crystal tracking ID 292651h10, unique puck ID ltv3-10
Crystal Properties Matthews coefficient Solvent content 2.6 52.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.6 α = 90 b = 86.98 β = 98.45 c = 124.13 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 MARMOSAIC 300 mm CCD 2017-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.6 38.734 98.4 0.049 0.057 0.999 14.33 3.994 214046 -3 20.65
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 88.1 0.452 0.54 0.851 2.09 3.013
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3s9z 1.6 38.734 1.34 213968 1995 98.35 0.1524 0.1522 0.1739 0.1879 29.5546
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.273 f_angle_d 0.814 f_chiral_restr 0.052 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11021 Nucleic Acid Atoms Solvent Atoms 1903 Heterogen Atoms 112
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing