2QUF
Crystal Structure of Transcription Factor AXXA-PF0095 from Pyrococcus furiosus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2PLZ | Pdb entry 2PLZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.8 | 291 | 70mM Sodium Acetate, 30% Glycerol, pH 4.8, modified microbatch, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48.75 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 39.747 | α = 90 |
b = 93.484 | β = 102.44 |
c = 71.062 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 2007-06-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-BM | 1.0 | APS | 22-BM |
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 | 2.8 | 32.53 | 98 | 0.058 | 6.6 | 11712 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.8 | 2.88 | 85 | 0.205 | 5.5 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | Pdb entry 2PLZ | 2.8 | 32.53 | 11712 | 11712 | 608 | 98 | 0.246 | 0.244 | 0.281 | RANDOM | 79.95 |
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] | |
-0.11 | -0.2 | 0.39 | -0.37 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.775 |
r_dihedral_angle_4_deg | 20.451 |
r_dihedral_angle_3_deg | 17.482 |
r_dihedral_angle_1_deg | 5.394 |
r_angle_refined_deg | 1.058 |
r_scangle_it | 0.915 |
r_mcangle_it | 0.684 |
r_scbond_it | 0.54 |
r_mcbond_it | 0.378 |
r_nbtor_refined | 0.297 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3324 |
Nucleic Acid Atoms | |
Solvent Atoms | 21 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SERGUI | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |