3NQH
Crystal structure of a glycosyl hydrolase (BT_2959) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.11 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 277 | 15.0000% Glycerol, 0.1700M NH4OAc, 25.5000% PEG-4000, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52.33 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.923 | α = 90 |
b = 78.923 | β = 90 |
c = 166.87 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | 2009-04-16 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.91837,0.97852,0.97802 | SSRL | BL11-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.11 | 29.801 | 99.9 | 0.119 | 0.119 | 10.9 | 6.3 | 31222 | 35.599 |
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) | ||||||||||
2.11 | 2.16 | 100 | 0.923 | 0.923 | 1.8 | 6.4 | 2248 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.11 | 29.801 | 31147 | 1564 | 99.85 | 0.197 | 0.195 | 0.238 | RANDOM | 47.063 |
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] | |
1.65 | 1.65 | -3.3 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.437 |
r_dihedral_angle_4_deg | 14.915 |
r_dihedral_angle_3_deg | 10.865 |
r_scangle_it | 5.238 |
r_scbond_it | 3.921 |
r_dihedral_angle_1_deg | 3.69 |
r_mcangle_it | 2.293 |
r_angle_refined_deg | 1.523 |
r_mcbond_it | 1.299 |
r_angle_other_deg | 0.848 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3444 |
Nucleic Acid Atoms | |
Solvent Atoms | 239 |
Heterogen Atoms | 16 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
SHELX | phasing |
MolProbity | model building |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
SHELXD | phasing |
autoSHARP | phasing |