1KG5
Crystal structure of the K142Q mutant of E.coli MutY (core fragment)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1KG2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 288 | Lithium sulfate, HEPES, Sodium chloride, Magnesium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.75 | 50.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 83.49 | α = 90 |
b = 50.12 | β = 122.68 |
c = 70.38 | 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 | 1999-09-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X26C | 1.100 | NSLS | X26C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.35 | 40 | 91.7 | 0.062 | 13.5 | 4.5 | 49330 | 49330 | 11.1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.35 | 1.37 | 55.4 | 0.214 | 2 | 1464 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | Difference fourier | FREE R | 1KG2 | 1.35 | 40 | 49330 | 49330 | 2456 | 91.7 | 0.1281 | 0.169 | RANDOM | 15.5 |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
9 | 2110 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_similar_dist | 0.077 |
s_approx_iso_adps | 0.071 |
s_non_zero_chiral_vol | 0.061 |
s_zero_chiral_vol | 0.052 |
s_angle_d | 0.031 |
s_similar_adp_cmpnt | 0.031 |
s_from_restr_planes | 0.0236 |
s_anti_bump_dis_restr | 0.017 |
s_bond_d | 0.016 |
s_rigid_bond_adp_cmpnt | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1761 |
Nucleic Acid Atoms | |
Solvent Atoms | 309 |
Heterogen Atoms | 37 |
Software
Software | |
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Software Name | Purpose |
SHELXL-97 | refinement |
SCALEPACK | data scaling |
CNS | refinement |
DENZO | data reduction |
CNS | phasing |