2PIJ
Structure of the Cro protein from prophage Pfl 6 in Pseudomonas fluorescens Pf-5
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 9.5 | 298 | primary precipitating solution: 2.2M ammonium sulfate, 0.1M tris additional chemicals in drop: 2mM dithiothreitol, 0.2mM EDTA, 0.01% sodium azide, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.02 | 38.96 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.94 | α = 90 |
b = 40.94 | β = 90 |
c = 123.5 | 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 | MARMOSAIC 325 mm CCD | flat collimating mirror double crystal monochromator toroid focusing mirror | 2005-07-21 | M | MAD | |||||
2 | 1 | |||||||||||||
3 | 1 |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.97935,0.97921,0.91165 | SSRL | BL9-2 |
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 | 1.7 | 34.08 | 98.1 | 0.055 | 13.5 | 4.84 | 13741 | 13741 | 39.3 |
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 | 1.7 | 1.76 | 90.7 | 0.434 | 3 | 4.28 | 1222 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 1.7 | 34.08 | 13741 | 13741 | 677 | 98.09 | 0.221 | 0.221 | 0.218 | 0.271 | RANDOM | 24.302 |
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] | |
0.76 | 0.38 | 0.76 | -1.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.48 |
r_dihedral_angle_4_deg | 23.688 |
r_dihedral_angle_3_deg | 15.701 |
r_dihedral_angle_1_deg | 6.084 |
r_scangle_it | 3.522 |
r_scbond_it | 2.517 |
r_angle_refined_deg | 1.855 |
r_mcangle_it | 1.586 |
r_mcbond_it | 1.197 |
r_nbtor_refined | 0.306 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 907 |
Nucleic Acid Atoms | |
Solvent Atoms | 61 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
d*TREK | data scaling |
SOLVE | phasing |
RESOLVE | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Blu-Ice | data collection |
CrystalClear | data reduction |
CrystalClear | data scaling |