1VR5
Crystal structure of Oligopeptide ABC transporter, periplasmic oligopeptide-binding (TM1223) from THERMOTOGA MARITIMA at 1.73 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 7 | 277 | 1.0M LiCl, 10.0% PEG-6000, 0.1M HEPES pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.79 | 55.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 140.03 | α = 90 |
b = 96.64 | β = 90 |
c = 115.78 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC | 2005-01-22 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.1 | 0.97933, 1.00003,0.97951 | ALS | 8.2.1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.73 | 28.61 | 99.9 | 0.087 | 10.3 | 3.8 | 163581 | 32.24 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.73 | 1.82 | 100 | 0.627 | 2.8 | 3.8 | 23624 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | MAD | THROUGHOUT | 1.73 | 28.61 | 155289 | 8214 | 99.85 | 0.15314 | 0.15164 | 0.18161 | RANDOM | 24.051 |
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] | |
1.63 | 0.6 | -2.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.68 |
r_dihedral_angle_4_deg | 16.847 |
r_dihedral_angle_3_deg | 11.412 |
r_scangle_it | 7.121 |
r_dihedral_angle_1_deg | 6.082 |
r_scbond_it | 5.03 |
r_mcangle_it | 3.083 |
r_mcbond_it | 1.963 |
r_angle_refined_deg | 1.554 |
r_angle_other_deg | 0.879 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8692 |
Nucleic Acid Atoms | |
Solvent Atoms | 1098 |
Heterogen Atoms | 161 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
SCALA | data scaling |
SHELXD | phasing |
SHARP | phasing |
REFMAC | refinement |
XDS | data reduction |
CCP4 | data scaling |