3LF0
Crystal structure of the ATP bound Mycobacterium tuberculosis nitrogen regulatory PII protein
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3BZQ | PDB ENTRY 3bzq |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 289 | 0.1 M Imidazole pH 6.0 and 1.0 M Sodium acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 69.742 | α = 90 |
b = 69.742 | β = 90 |
c = 146.682 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 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 | 120 | CCD | MARMOSAIC 300 mm CCD | 2005-10-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 0.97953 | APS | 23-ID-B |
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 | 2.4 | 62.99 | 99.78 | 0.07 | 12.2 | 14020 | 14020 |
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) | |||||||||||
2.4 | 2.464 | 97.92 | 0.63 | 2.02 |
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 3bzq | 2.4 | 62.99 | 14020 | 14020 | 744 | 99.78 | 0.20752 | 0.20418 | 0.27246 | RANDOM | 42.537 |
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] | |
0.35 | 0.35 | -0.69 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.058 |
r_dihedral_angle_3_deg | 19.798 |
r_dihedral_angle_4_deg | 18.902 |
r_dihedral_angle_1_deg | 6.331 |
r_scangle_it | 3.696 |
r_scbond_it | 2.214 |
r_angle_refined_deg | 1.86 |
r_mcangle_it | 1.215 |
r_mcbond_it | 0.733 |
r_nbtor_refined | 0.301 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2361 |
Nucleic Acid Atoms | |
Solvent Atoms | 124 |
Heterogen Atoms | 93 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
CCP4 | model building |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CCP4 | phasing |