3P4E
Phosphoribosylformylglycinamidine cyclo-ligase from Vibrio cholerae
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.3 | 289 | 0.2 M ammonium-citrate dibasic, 20% PEG 3350, pH 4.3, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 54.42 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 106.277 | α = 90 |
b = 106.277 | β = 90 |
c = 61.379 | γ = 120 |
Symmetry | |
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Space Group | P 32 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 | 2010-08-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.9792 | APS | 19-ID |
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 | 1.77 | 40.2 | 100 | 0.051 | 10.7 | 6.9 | 39208 | 39208 | 37.7 |
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) | |||||||||||
1.77 | 1.8 | 100 | 0.682 | 2.05 | 5.8 | 1946 |
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 | 1CLI | 1.77 | 40.17 | 39087 | 39087 | 1966 | 99.67 | 0.1502 | 0.1502 | 0.1489 | 0.175 | RANDOM | 29.635 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.59 | 0.29 | 0.59 | -0.88 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.03 |
r_dihedral_angle_4_deg | 19.937 |
r_dihedral_angle_3_deg | 14.735 |
r_dihedral_angle_1_deg | 6.175 |
r_scangle_it | 4.406 |
r_scbond_it | 2.72 |
r_mcangle_it | 1.746 |
r_angle_refined_deg | 1.703 |
r_angle_other_deg | 0.99 |
r_mcbond_it | 0.956 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2426 |
Nucleic Acid Atoms | |
Solvent Atoms | 282 |
Heterogen Atoms | 46 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SBC-Collect | data collection |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
MOLREP | phasing |
HKL-3000 | phasing |