3HT6
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 |
2.76 | 55.43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.281 | α = 90 |
b = 60.281 | β = 90 |
c = 98.11 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.41 | 50 | 92.8 | 0.081 | 33.152 | 7.8 | 37764 | 37764 |
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) | |||||||||||
1.41 | 1.46 | 41 | 0.496 | 0.0424 | 2 | 1640 |
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 | 1.59 | 50 | 28308 | 28308 | 1443 | 99.75 | 0.184 | 0.184 | 0.182 | 0.22 | RANDOM | 18.412 |
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] | |
-0.13 | -0.06 | -0.13 | 0.19 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.726 |
r_dihedral_angle_4_deg | 14.771 |
r_dihedral_angle_3_deg | 11.793 |
r_dihedral_angle_1_deg | 5.15 |
r_scangle_it | 2.605 |
r_scbond_it | 1.806 |
r_angle_refined_deg | 1.133 |
r_mcangle_it | 0.969 |
r_mcbond_it | 0.646 |
r_nbtor_refined | 0.309 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1342 |
Nucleic Acid Atoms | |
Solvent Atoms | 293 |
Heterogen Atoms | 26 |
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 |