5D6A
2.7 Angstrom Crystal Structure of ABC transporter ATPase from Vibrio vulnificus in Complex with Adenylyl-imidodiphosphate (AMP-PNP)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5 | 295 | Protein: 5.9 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3), 1mM AMPPNP; Screen: PACT (C2), 0.1M PCB buffer (pH 5.0), 25% (w/v) PEG 1500 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 104.957 | α = 90 |
b = 104.957 | β = 90 |
c = 85.354 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 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 225 mm CCD | 2014-11-17 | 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) | 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 | 2.7 | 30 | 100 | 0.117 | 0.117 | 32.5 | 11 | 15243 | 15243 | -3 | 57.9 |
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 | 2.7 | 2.75 | 100 | 0.621 | 5 | 11.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 2.7 | 28.55 | 13687 | 1535 | 99.8 | 0.19991 | 0.1941 | 0.25555 | RANDOM | 55.709 |
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] | |
-0.15 | -0.08 | -0.15 | 0.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 22.501 |
r_dihedral_angle_4_deg | 7.935 |
r_dihedral_angle_3_deg | 7.764 |
r_long_range_B_refined | 4.125 |
r_long_range_B_other | 4.086 |
r_mcangle_it | 2.049 |
r_mcangle_other | 2.049 |
r_scangle_other | 1.928 |
r_dihedral_angle_1_deg | 1.771 |
r_mcbond_it | 1.156 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4297 |
Nucleic Acid Atoms | |
Solvent Atoms | 84 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
BLU-MAX | data collection |
HKL-3000 | phasing |
HKL-3000 | data scaling |
PHENIX | phasing |