3KZS
Crystal structure of glycosyl hydrolase family 5 (NP_809925.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 0.20M ammonium sulfate, 40.0% 2-methyl-2,4-pentanediol, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.77 | 55.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 261.335 | α = 90 |
b = 261.335 | β = 90 |
c = 183.87 | γ = 120 |
Symmetry | |
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Space Group | H 3 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 | MARMOSAIC 325 mm CCD | Flat mirror (vertical focusing) | 2008-11-13 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.91162,0.97870,0.97814 | SSRL | BL11-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 85.176 | 100 | 0.124 | 11.7 | 6.4 | 139171 | 139171 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.1 | 2.21 | 99.9 | 0.656 | 0.656 | 1.1 | 6.4 | 20050 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 2.1 | 85.176 | 139161 | 6991 | 99.99 | 0.187 | 0.185 | 0.222 | RANDOM | 27.854 |
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] | |
0.36 | 0.18 | 0.36 | -0.54 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.124 |
r_dihedral_angle_3_deg | 9.459 |
r_dihedral_angle_4_deg | 8.361 |
r_dihedral_angle_1_deg | 3.197 |
r_scangle_it | 2.392 |
r_scbond_it | 1.631 |
r_mcangle_it | 1.001 |
r_angle_refined_deg | 0.843 |
r_angle_other_deg | 0.629 |
r_mcbond_it | 0.544 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14947 |
Nucleic Acid Atoms | |
Solvent Atoms | 1208 |
Heterogen Atoms | 160 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
SHELX | phasing |
SHARP | phasing |
REFMAC | refinement |
MolProbity | model building |
PDB_EXTRACT | data extraction |
SHELXD | phasing |
autoSHARP | phasing |