4F3P
Crystal structure of a Glutamine-binding periplasmic protein from Burkholderia pseudomallei in complex with glutamine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GGG | pdb entry 1ggg modified with CCP4 program chainsaw |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 290 | MD Morpheus screen C12: 12.5% PEG 3350, 12.5% PEG 1000, 12.5% MPD, 30mM sodium nitrate, 30mM disodium hydrgon phosphate, 30mM ammonium sulphate, 100mM bicine/trizma; BupsA.17285.b.A2 PW PS01148 20mg/ml, tray 232242c12, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.83 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.33 | α = 90 |
b = 74.5 | β = 100.63 |
c = 60.19 | 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 | ADSC QUANTUM 315r | 2012-04-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 0.9774 | ALS | 5.0.1 |
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 | 2.4 | 50 | 99.9 | 0.086 | 14.36 | 3.8 | 19275 | 19249 | -3 | 37.414 |
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 | 2.4 | 2.46 | 99.6 | 0.524 | 2.6 | 3.8 |
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 1ggg modified with CCP4 program chainsaw | 2.4 | 50 | 19249 | 19235 | 986 | 99.93 | 0.1789 | 0.1789 | 0.1769 | 0.2152 | RANDOM | 30.518 |
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] | |
-0.35 | 0.5 | 0.3 | 0.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 42.528 |
r_dihedral_angle_4_deg | 18.63 |
r_dihedral_angle_3_deg | 13.939 |
r_dihedral_angle_1_deg | 6.272 |
r_angle_refined_deg | 1.588 |
r_angle_other_deg | 1.166 |
r_chiral_restr | 0.088 |
r_bond_refined_d | 0.014 |
r_gen_planes_refined | 0.007 |
r_bond_other_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3345 |
Nucleic Acid Atoms | |
Solvent Atoms | 128 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
StructureStudio | data collection |
XDS | data reduction |