3P3K
The crystal structure of translationally controlled tumor protein (TCTP) of Plasmodium falciparum
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1TXJ | PDB ENTRY 1TXJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 277.15 | 21.5 % PEG 4000, 1,6-hexanediol, 50 mM bis-tris methane, 50mM magnesium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.47 | 50.18 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.858 | α = 90 |
b = 61.858 | β = 90 |
c = 111.684 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 | IMAGE PLATE | MAR scanner 300 mm plate | Graphite Monochromator | 2009-03-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | ENRAF-NONIUS FR591 | 1.5418 |
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 | 2.55 | 29.8 | 99 | 0.056 | 4.9 | 7436 | 1 | 1 | 50.1 |
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 | 2.55 | 2.59 | 98.2 | 0.182 | 7.6 | 5.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | 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 | PDB ENTRY 1TXJ | 2.551 | 29.8 | 1.34 | 7455 | 7436 | 342 | 98.53 | 0.2169 | 0.2157 | 0.2402 | RANDOM | 32 |
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] | |
-3.2733 | -3.2733 | 6.5465 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.603 |
f_angle_d | 0.589 |
f_chiral_restr | 0.046 |
f_bond_d | 0.002 |
f_plane_restr | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1352 |
Nucleic Acid Atoms | |
Solvent Atoms | 66 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
MOLREP | phasing |
PHENIX | refinement |
MOSFLM | data reduction |
SCALA | data scaling |