3HT8
5-chloro-2-methylphenol in complex with T4 lysozyme L99A/M102Q
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1LGU | PDB entry 1LGU |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 2.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 6.5, vapor diffusion, hanging drop, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.77 | 55.53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.48 | α = 90 |
b = 60.48 | β = 90 |
c = 97.68 | γ = 120 |
Symmetry | |
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Space Group | P 32 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 | 296 | CCD | ADSC QUANTUM 315r | 2008-07-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.11589 | ALS | 8.3.1 |
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 | 1.46 | 50 | 92.7 | 0.071 | 37.605 | 5.7 | 34328 | 34328 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.46 | 1.51 | 45.7 | 0.716 | 2.46 | 2.4 | 1663 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | REFMAC | THROUGHOUT | PDB entry 1LGU | 1.6 | 50 | 27904 | 27904 | 1414 | 99.89 | 0.19 | 0.19 | 0.188 | 0.214 | RANDOM | 21.809 |
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] | |
0.82 | 0.41 | 0.82 | -1.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.801 |
r_dihedral_angle_4_deg | 16.78 |
r_dihedral_angle_3_deg | 13.174 |
r_dihedral_angle_1_deg | 5.018 |
r_scangle_it | 2.869 |
r_scbond_it | 1.965 |
r_angle_refined_deg | 1.193 |
r_mcangle_it | 1.118 |
r_mcbond_it | 0.746 |
r_nbtor_refined | 0.307 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1292 |
Nucleic Acid Atoms | |
Solvent Atoms | 245 |
Heterogen Atoms | 19 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
REFMAC | phasing |