2D30
Crystal Structure of Cytidine Deaminase Cdd-2 (BA4525) from Bacillus Anthracis at 2.40A Resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 291 | PEG2000 MME, Ca_acetate, TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 45.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 99.792 | α = 90 |
b = 50.552 | β = 132.1 |
c = 70.438 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 4 | Rh coated Si mirror | 2004-11-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX9.6 | 0.87000 | SRS | PX9.6 |
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 | 50 | 92.7 | 0.074 | 15.5 | 3.5 | 9578 | 9578 |
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 | 2.4 | 2.49 | 62.1 | 0.172 | 5.7 | 2.5 | 630 |
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 | 1JTK | 2.4 | 27.89 | 9117 | 9117 | 458 | 100 | 0.16825 | 0.16825 | 0.16429 | 0.25075 | RANDOM | 30.112 |
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] | |
-0.63 | 1.05 | -0.02 | 2.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 42.25 |
r_dihedral_angle_3_deg | 19.541 |
r_dihedral_angle_4_deg | 15.845 |
r_scangle_it | 6.865 |
r_dihedral_angle_1_deg | 5.821 |
r_scbond_it | 5.075 |
r_mcangle_it | 2.822 |
r_mcbond_it | 2.091 |
r_angle_refined_deg | 1.693 |
r_angle_other_deg | 0.93 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1880 |
Nucleic Acid Atoms | |
Solvent Atoms | 135 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |