3FCY
Crystal Structure of Acetyl Xylan Esterase 1 from Thermoanaerobacterium sp. JW/SL YS485
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3FVR | PDB entry 3FVR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 7.5 | 293 | 14% PEG 400, 0.1M calcium chloride, 0.05M sodium HEPES, pH 7.5, microbatch, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.41 | 49.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 132.263 | α = 90 |
b = 132.263 | β = 90 |
c = 112.914 | 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 | 100 | CCD | ADSC QUANTUM 4 | 2005-09-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 0.9786 | ESRF | ID14-4 |
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 | 2.1 | 25 | 100 | 0.067 | 11.1 | 66742 | 66742 | -3 | 27.56 |
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) | |||||||||||
2.1 | 2.14 | 100 | 0.329 | 2.3 | 10.6 | 3296 |
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-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 3FVR | 2.1 | 25 | 66710 | 66710 | 6761 | 100 | 0.184 | 0.184 | 0.184 | 0.212 | RANDOM | 28 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
2.705 | 0.702 | 2.705 | -5.41 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_scangle_it | 2.894 |
c_scbond_it | 1.983 |
c_mcangle_it | 1.584 |
c_angle_deg | 1.253 |
c_mcbond_it | 1.124 |
c_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7572 |
Nucleic Acid Atoms | |
Solvent Atoms | 489 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |
CNS | refinement |
PDB_EXTRACT | data extraction |
ProDC | data collection |