2C9B
Lumazine Synthase from Mycobacterium tuberculosus Bound to 3-(1,3,7- TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.4 | pH 6.40 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 50 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.045 | α = 64.39 |
b = 78.364 | β = 64.69 |
c = 88.843 | γ = 65.03 |
Symmetry | |
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Space Group | P 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 | 105 | IMAGE PLATE | MARRESEACH | MIRRORS | 2005-05-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | ROTATING ANODE |
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 | 2.65 | 15 | 89.1 | 0.15 | 4.4 | 2.5 | 59532 | 1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.65 | 2.71 | 85.7 | 0.48 | 1.25 | 1.5 |
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 1W19 | 2.75 | 10 | 35562 | 1897 | 89.5 | 0.254 | 0.25 | 0.324 | RANDOM | 32.84 |
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] | |
0.74 | -1.17 | -0.08 | -0.1 | 1.23 | -0.65 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.744 |
r_dihedral_angle_3_deg | 15.492 |
r_dihedral_angle_4_deg | 15.329 |
r_dihedral_angle_1_deg | 4.16 |
r_angle_refined_deg | 1.168 |
r_nbtor_refined | 0.285 |
r_nbd_refined | 0.185 |
r_symmetry_vdw_refined | 0.174 |
r_symmetry_hbond_refined | 0.142 |
r_xyhbond_nbd_refined | 0.125 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10598 |
Nucleic Acid Atoms | |
Solvent Atoms | 654 |
Heterogen Atoms | 291 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |