3NVS
1.02 Angstrom resolution crystal structure of 3-phosphoshikimate 1-carboxyvinyltransferase from Vibrio cholerae in complex with shikimate-3-phosphate (partially photolyzed) and glyphosate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1G6S | PDB ENTRY 1G6S |
Crystallization
Crystalization Experiments | ||||
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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 | |
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Matthews coefficient | Solvent content |
1.89 | 35.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43.866 | α = 90 |
b = 87.484 | β = 105.26 |
c = 49.994 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 0.82648 | APS | 21-ID-D |
Data Collection
Overall | |||||||||||||||||||
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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 | |||||||||||||||||||
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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 | |||||||||||||||||||
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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 | R-Free | 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 | 0.13767 | RANDOM | 8.505 |
Temperature Factor Modeling | ||||||
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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 | |
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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 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3240 |
Nucleic Acid Atoms | |
Solvent Atoms | 747 |
Heterogen Atoms | 65 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |