5J6F
Crystal structure of DAH7PS-CM complex from Geobacillus sp. with prephenate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3TFC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 6.5 | 298 | A protein solution (11 mg/mL in 20 mM BTP, 40 mM KCl, 200 ??M PEP, pH 7.4) was mixed 1:1 (v/v) with a reservoir solution containing 0.2 M sodium citrate, 0.1 M BTP, pH 6.5, 20% W/V PEG 3350 and 0.2 mM chorismic acid. 2 ??L drop size. 500 ??L reservoir volume. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.66 | 53.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 95.438 | α = 90 |
b = 95.438 | β = 90 |
c = 167.452 | γ = 120 |
Symmetry | |
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Space Group | P 64 |
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 | 110 | CCD | ADSC QUANTUM 315r | 2012-04-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.953700 | Australian Synchrotron | MX2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.75 | 82.65 | 99.9 | 0.079 | 1 | 18 | 7.6 | 22482 |
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 | 2.75 | 2.88 | 100 | 1.336 | 7.7 |
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 | 3TFC | 2.75 | 82.65 | 21178 | 1054 | 99.02 | 0.18471 | 0.18221 | 0.2352 | RANDOM | 77.759 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
-0.49 | -0.24 | -0.49 | 1.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.677 |
r_dihedral_angle_3_deg | 18.841 |
r_dihedral_angle_4_deg | 16.568 |
r_long_range_B_other | 7.983 |
r_long_range_B_refined | 7.981 |
r_dihedral_angle_1_deg | 6.922 |
r_scangle_other | 6.26 |
r_mcangle_it | 4.289 |
r_mcangle_other | 4.289 |
r_scbond_it | 3.895 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5366 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 54 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |
XDS | data reduction |