2X9G
High resolution structure of TbPTR1 in complex with Pemetrexed
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | RESERVOIR CONDITIONS: 100 MM SODIUM CITRATE PH 5, 1.8 M SODIUM ACETATE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.83 | 32.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.72 | α = 90 |
b = 90.57 | β = 115.61 |
c = 82.58 | 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 CCD | 2007-12-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | ESRF | ID14-4 |
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 | 1.1 | 41.8 | 98.7 | 0.05 | 15.6 | 4.3 | 396089 |
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 | 1.1 | 1.2 | 96.7 | 0.29 | 4.4 | 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 (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | OTHER | FREE R-VALUE | NONE | 1.1 | 20 | 396089 | 17155 | 94.7 | 0.1206 | 0.1468 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
138 | 6987.7 | 9153.57 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_approx_iso_adps | 0.102 |
s_non_zero_chiral_vol | 0.093 |
s_zero_chiral_vol | 0.078 |
s_anti_bump_dis_restr | 0.07 |
s_similar_adp_cmpnt | 0.033 |
s_angle_d | 0.031 |
s_from_restr_planes | 0.0273 |
s_bond_d | 0.014 |
s_rigid_bond_adp_cmpnt | 0.005 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7462 |
Nucleic Acid Atoms | |
Solvent Atoms | 1372 |
Heterogen Atoms | 320 |
Software
Software | |
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Software Name | Purpose |
SHELXL-97 | refinement |
XDS | data reduction |
XSCALE | data scaling |