4F3W
Crystal structure of cytidine deaminase Cdd from Mycobacterium marinum
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 289 | MymaA.00495.a.A1 PS00823 at 20 mg/mL against JCSG+ A8 0.2 M sodium formate, 20% PEG 3350, crystal tracking ID 232847a8, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2 | 38.43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 47.47 | α = 100.19 |
b = 48.71 | β = 110.42 |
c = 53.92 | γ = 98.39 |
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 | 100 | CCD | RIGAKU SATURN 944+ | 2012-05-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
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 | 1.8 | 50 | 99.1 | 0.04 | 25.76 | 5 | 40341 | 39961 | -3 | 24.135 |
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 | 1.8 | 1.85 | 96.1 | 0.181 | 5.98 |
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 3ijf | 1.8 | 48.98 | 39960 | 1977 | 99.31 | 0.182 | 0.1801 | 0.2181 | RANDOM | 18.0363 |
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] | |
0.4 | 0.31 | 0.42 | 0.08 | 0.04 | -0.08 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.73 |
r_dihedral_angle_4_deg | 15.459 |
r_dihedral_angle_3_deg | 13.433 |
r_dihedral_angle_1_deg | 5.514 |
r_angle_refined_deg | 1.478 |
r_angle_other_deg | 0.941 |
r_chiral_restr | 0.086 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.007 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3437 |
Nucleic Acid Atoms | |
Solvent Atoms | 299 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
StructureStudio | data collection |
XDS | data reduction |