4ROT
Crystal structure of esterase A from Streptococcus pyogenes
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 0.1 M HEPES, 20% PEG4000, 10% 2-propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.93 | 57.96 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 103.98 | α = 90 |
b = 103.98 | β = 90 |
c = 133.631 | γ = 90 |
Symmetry | |
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Space Group | I 4 2 2 |
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 210 | Toroidal Mirror | 2005-09-24 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 210 | Toroidal Mirror | 2005-09-24 | M | SINGLE WAVELENGTH | |||||
3 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 210 | Toroidal Mirror | 2005-09-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.93937 | ESRF | ID29 |
2 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.93957 | ESRF | ID29 |
3 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.89844 | ESRF | ID29 |
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 | ||||||||
1,2,3 | 1.75 | 15 | 99.8 | 0.081 | 10.4 | 37068 | 37068 | 13.9 |
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) | |||||||||||
1,2,3 | 1.75 | 1.81 | 99.9 | 0.496 | 3658 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 1.8 | 14.89 | 34036 | 32310 | 1724 | 99.46 | 0.15941 | 0.15941 | 0.15759 | 0.19319 | RANDOM | 14.426 |
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] | |
0.03 | 0.03 | -0.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.779 |
r_dihedral_angle_4_deg | 15.746 |
r_dihedral_angle_3_deg | 14.807 |
r_dihedral_angle_1_deg | 6.79 |
r_long_range_B_refined | 6.317 |
r_long_range_B_other | 5.957 |
r_scangle_other | 3.809 |
r_mcangle_it | 2.625 |
r_mcangle_other | 2.624 |
r_scbond_other | 2.46 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2173 |
Nucleic Acid Atoms | |
Solvent Atoms | 325 |
Heterogen Atoms | 7 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
SOLVE | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |