5XB5
Crystal structure of R90A mutant of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2PBR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 7.5 | 293 | 0.1M HEPES, 10% w/v Polyethylene glycol 8000, 8% v/v Ethylene glycol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.46 | 50.05 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43.01 | α = 92.17 |
b = 51.84 | β = 92.67 |
c = 53.64 | γ = 112.83 |
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 | IMAGE PLATE | MAR scanner 345 mm plate | 2012-04-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 2.21 | 53.48 | 93 | 0.1 | 0.996 | 11.8 | 4.3 | 19751 | 28.3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.21 | 2.29 | 68.6 | 0.554 | 0.851 | 2.3 | 3.9 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2PBR | 2.23 | 53.48 | 18753 | 991 | 95.01 | 0.24266 | 0.24035 | 0.28591 | RANDOM | 55.258 |
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] | |
-6.6 | 2.88 | -0.2 | 4.73 | 2.66 | -2.7 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.171 |
r_dihedral_angle_4_deg | 20.844 |
r_dihedral_angle_3_deg | 17.441 |
r_dihedral_angle_1_deg | 7.354 |
r_long_range_B_refined | 4.902 |
r_long_range_B_other | 4.902 |
r_angle_refined_deg | 1.855 |
r_angle_other_deg | 1.136 |
r_mcangle_it | 1.024 |
r_mcangle_other | 1.024 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2974 |
Nucleic Acid Atoms | |
Solvent Atoms | 38 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
iMOSFLM | data reduction |
Aimless | data scaling |
MOLREP | phasing |