3QYQ
1.8 Angstrom resolution crystal structure of a putative deoxyribose-phosphate aldolase from Toxoplasma gondii ME49
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2A4A |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4 | 277 | Protein at 7 mg/mL in 10 mM Tris/HCl, pH=8.3, 0.5 M NaCl, 5 mM BME. Crystallization condition: 0.1 M Citric acid, pH=4.0, 0.8 M Ammonium sulfate (The AmSO4 suite, condition E1 (49)). Cryo condition: 1:1 v/v 50 % sucrose:E1 condition , VAPOR DIFFUSION, SITTING DROP, temperature 277 and 287K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.61 | 52.84 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 70.923 | ¦Á = 62.9 |
b = 72.194 | ¦Â = 89.8 |
c = 73.048 | ¦Ã = 88.85 |
Symmetry | |
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Space Group | P 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 | Be-Lenses/Diamond Laue Mono | 2011-02-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
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 | 1.8 | 30 | 97.6 | 0.063 | 14.66 | 3.1 | 116483 | 116483 | -3 |
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 | 1.8 | 1.83 | 96.2 | 0.495 | 2.36 | 3.1 |
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 (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2A4A | 1.8 | 29.49 | 110552 | 110552 | 5879 | 97.26 | 0.1674 | 0.16568 | 0.18 | 0.2006 | 0.21 | RANDOM | 32.566 |
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] | |
1.21 | -0.87 | 1.07 | 1.22 | -0.91 | -1.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 20.73 |
r_dihedral_angle_4_deg | 8.177 |
r_dihedral_angle_3_deg | 7.081 |
r_scangle_it | 5.102 |
r_scbond_it | 3.069 |
r_mcangle_it | 1.896 |
r_dihedral_angle_1_deg | 1.481 |
r_angle_refined_deg | 1.464 |
r_mcbond_it | 1.034 |
r_angle_other_deg | 0.827 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8272 |
Nucleic Acid Atoms | |
Solvent Atoms | 927 |
Heterogen Atoms | 149 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |