3INP
2.05 Angstrom Resolution Crystal Structure of D-ribulose-phosphate 3-epimerase from Francisella tularensis.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1TQJ | PDB entry 1TQJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4 | 295 | protein solution: 7.5 mg/mL, 0.5M Sodium chloride, TRIS-HCl pH 8.3; Screen solution: JCSG+, condition B1, 0.8M Ammonium sulfate, 0.1M Citric acid pH 4.0; Cryo solution: 1.8M Ammonium sulfate, 25% (w/v) Sucrose., VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.37 | 71.86 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 224.08 | α = 90 |
b = 224.08 | β = 90 |
c = 224.08 | γ = 90 |
Symmetry | |
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Space Group | F 41 3 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 | CCD | MARMOSAIC 225 mm CCD | Diamond | 2009-08-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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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 | 2.05 | 30 | 100 | 0.096 | 28.2 | 14.4 | 30690 | 30690 | -3 | 29.9 |
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 | 2.05 | 2.09 | 100 | 0.472 | 6.3 | 14.6 | 1518 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1TQJ | 2.05 | 29.94 | 29116 | 29116 | 1548 | 99.99 | 0.15925 | 0.15925 | 0.15833 | 0.17703 | RANDOM | 13.424 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.981 |
r_dihedral_angle_4_deg | 20.55 |
r_dihedral_angle_3_deg | 9.932 |
r_scangle_it | 5.058 |
r_scbond_it | 3.265 |
r_dihedral_angle_1_deg | 3.121 |
r_mcangle_it | 1.773 |
r_angle_refined_deg | 1.396 |
r_mcbond_it | 1.004 |
r_angle_other_deg | 0.866 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1663 |
Nucleic Acid Atoms | |
Solvent Atoms | 165 |
Heterogen Atoms | 12 |
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 |