3UCA
Crystal structure of isoprenoid synthase (target EFI-501974) from clostridium perfringens
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3KRF | PDB ENTRY 3KRF |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.5 | 0.1M BIS-TRIS, 0.2M SODIUM CHLORIDE, PH 5.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.86 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.117 | α = 90 |
b = 70.117 | β = 90 |
c = 228.136 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 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 QUANTUM 315 | MIRRORS | 2011-10-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | NSLS | X29A |
Data Collection
Overall | |||||||||||||||||||
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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 | 2 | 50 | 99.8 | 0.132 | 5.7 | 7.2 | 45199 | -5 | 36.585 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2 | 2.03 | 100 | 1.1 | 6.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3KRF | 2 | 36.48 | 43574 | 1402 | 99.83 | 0.19059 | 0.18925 | 0.22996 | RANDOM | 47.279 |
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] | |
-0.38 | -0.19 | -0.38 | 0.57 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.34 |
r_dihedral_angle_3_deg | 16.217 |
r_dihedral_angle_4_deg | 12.332 |
r_scangle_it | 11.339 |
r_scbond_it | 7.746 |
r_mcangle_it | 5.325 |
r_dihedral_angle_1_deg | 4.468 |
r_mcbond_it | 3.584 |
r_angle_refined_deg | 1.109 |
r_chiral_restr | 0.076 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4240 |
Nucleic Acid Atoms | |
Solvent Atoms | 213 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |