5UYY
Crystal structure of prephenate dehydrogenase tyrA from Bacillus anthracis in complex with L-tyrosine
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 289 | 0.2 ul of 19 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% Glycerol, and 10 mM BME were mixed with 0.2 ul of the MCSG Suite 1 condition #11 (0.1 M MES pH=6.5, 0.2 M Magnesium chloride, 10% w/v PEG 4000) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). His-tag was removed prior to crystallization. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 84.682 | α = 90 |
b = 105.588 | β = 90 |
c = 179.625 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | Beryllium Lenses | 2014-07-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.6 | 50 | 99.9 | 0.069 | 0.069 | 0.071 | 0.027 | 8.2 | 7.4 | 50884 | -3 | 71.2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.6 | 2.64 | 100 | 0.963 | 0.374 | 0.803 | 2.1 | 7.5 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3GGG | 2.6 | 50 | 47834 | 2466 | 99.93 | 0.1913 | 0.1886 | 0.2461 | RANDOM | 76.618 |
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 | -1.19 | 1.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.506 |
r_dihedral_angle_3_deg | 17.361 |
r_dihedral_angle_4_deg | 15.182 |
r_dihedral_angle_1_deg | 6.149 |
r_angle_refined_deg | 1.732 |
r_angle_other_deg | 1.581 |
r_chiral_restr | 0.093 |
r_bond_refined_d | 0.016 |
r_gen_planes_refined | 0.01 |
r_bond_other_d | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11332 |
Nucleic Acid Atoms | |
Solvent Atoms | 506 |
Heterogen Atoms | 52 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data collection |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
MOLREP | phasing |
HKL-3000 | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
DENZO | data reduction |
SCALEPACK | data scaling |