3IJF
Crystal structure of cytidine deaminase from Mycobacterium tuberculosis
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2FR5 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 100 mM HEPES and 4.3 M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.35 | 47.59 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 63.705 | ¦Á = 90 |
| b = 75.338 | ¦Â = 90 |
| c = 55.116 | ¦Ã = 90 |
| Symmetry | |
|---|---|
| Space Group | C 2 2 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | IMAGE PLATE | MAC Science DIP-3000 | 2009-02-07 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | LNLS BEAMLINE D03B-MX1 | 1.437 | LNLS | D03B-MX1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.99 | 22.27 | 97 | 0.086 | 0.086 | 10 | 2.3 | 20845 | 9374 | 2 | 2 | ||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 2fr5 | 1.99 | 18.24 | 9374 | 8621 | 433 | 96.99 | 0.19264 | 0.19017 | 0.24015 | RANDOM | 17.537 | |||||
| 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] | |
| 0.01 | -0.01 | |||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.68 |
| r_dihedral_angle_3_deg | 20.873 |
| r_dihedral_angle_4_deg | 17.69 |
| r_dihedral_angle_1_deg | 5.942 |
| r_scangle_it | 4.037 |
| r_scbond_it | 2.855 |
| r_angle_refined_deg | 2.161 |
| r_mcangle_it | 1.658 |
| r_mcbond_it | 0.974 |
| r_nbtor_refined | 0.312 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 893 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 89 |
| Heterogen Atoms | 1 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-3000 | data collection |
| AMoRE | phasing |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
