2VYO
Chitin deacetylase family member from Encephalitozoon cuniculi
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2C1G | PDB ENTRY 2C1G |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | 293 | 10% PEG 8000, 100 MM IMIDAZOLE 200 MM CALCIUM ACETATE 10MM ZNCL 20C, pH 8.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.975 | α = 90 |
b = 81.916 | β = 90 |
c = 39.201 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 190 | CCD | ADSC CCD | TOROIDAL ZERODUR MIRROR | 2005-12-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | ESRF | ID14-2 |
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 | 1.5 | 20 | 99.5 | 0.05 | 19.5 | 3.4 | 33981 | 2.2 |
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 | 1.5 | 1.55 | 97.8 | 0.37 | 2.26 | 3.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2C1G | 1.5 | 20 | 33245 | 703 | 99.2 | 0.198 | 0.198 | 0.215 | RANDOM | 22.83 |
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] | |
-1.38 | 2.24 | -0.86 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.799 |
r_dihedral_angle_4_deg | 14.502 |
r_dihedral_angle_3_deg | 11.396 |
r_dihedral_angle_1_deg | 5.498 |
r_scangle_it | 3.322 |
r_scbond_it | 2.23 |
r_mcangle_it | 1.428 |
r_angle_refined_deg | 1.38 |
r_mcbond_it | 0.926 |
r_symmetry_vdw_refined | 0.311 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1599 |
Nucleic Acid Atoms | |
Solvent Atoms | 154 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |