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1.02 Angstrom resolution crystal structure of 3-phosphoshikimate 1-carboxyvinyltransferase from Vibrio cholerae in complex with shikimate-3-phosphate (partially photolyzed) and glyphosate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G6S PDB ENTRY 1G6S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 Protein: 4.0 mGr/mL, 0.25M Sodium cloride, 0.01M Tris-HCl (pH 8.3), 2mM Glyphosate, 1mM Shikimate-3-phosphate;
Screen: Classics II (G12), 0.2M Magnesium chloride, 0.1M HEPES (pH 7.5), 25% (w/v) PEG3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.89 35.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.866 α = 90 b = 87.484 β = 105.26 c = 49.994 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 Mirrors 2010-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.82648 APS 21-ID-D
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 1.02 15 97.2 0.044 16.3 2.2 178530 178530 -3 6.7
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) 1.02 1.04 95.5 0.391 2.2 2.2 8695
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1G6S 1.021 14.89 169410 169410 8975 97.17 0.11525 0.11525 0.11406 0.114 0.13767 0.1357 RANDOM 8.505
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] -0.39 -0.21 0.2 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.345 r_dihedral_angle_4_deg 16.118 r_dihedral_angle_3_deg 10.672 r_dihedral_angle_1_deg 5.421 r_scangle_it 5.008 r_scbond_it 3.523 r_mcangle_it 2.363 r_mcbond_other 2.137 r_rigid_bond_restr 1.808 r_mcbond_it 1.687
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.345 r_dihedral_angle_4_deg 16.118 r_dihedral_angle_3_deg 10.672 r_dihedral_angle_1_deg 5.421 r_scangle_it 5.008 r_scbond_it 3.523 r_mcangle_it 2.363 r_mcbond_other 2.137 r_rigid_bond_restr 1.808 r_mcbond_it 1.687 r_angle_refined_deg 1.542 r_angle_other_deg 0.979 r_chiral_restr 0.099 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3240 Nucleic Acid Atoms Solvent Atoms 747 Heterogen Atoms 65
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling