3O61
Structure of the E100A E.coli GDP-mannose hydrolase (yffh) in complex with GDP-mannose and Mg++
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 291 | 20-26% PEG 3350, 0.2 M Mg Cl, 0.1 M Tris HCL pH 8.5, 4mM GDP-mannose at a ratio of 1:1 protein:reservoir, vapor diffusion, hanging drop, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.75 | 55.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.276 | α = 90 |
b = 55.824 | β = 91.71 |
c = 158.121 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | ADSC QUANTUM 210 | 2009-10-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X6A | 0.9787 | NSLS | X6A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.45 | 32.4 | 93 | 0.098 | 14.4 | 3.2 | 32636 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
2.45 | 2.49 | 59 | 0.165 | 1.8 | 1030 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 3O52 | 2.45 | 32.4 | 32614 | 1644 | 92.73 | 0.2273 | 0.2239 | 0.2902 | RANDOM | 53.14 |
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] | |
-6.3 | 1.64 | 7.41 | -1.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.857 |
r_dihedral_angle_3_deg | 18.397 |
r_dihedral_angle_4_deg | 16.159 |
r_dihedral_angle_1_deg | 6.714 |
r_scangle_it | 2.627 |
r_scbond_it | 1.697 |
r_angle_refined_deg | 1.584 |
r_mcangle_it | 1.052 |
r_mcbond_it | 0.575 |
r_nbtor_refined | 0.315 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5971 |
Nucleic Acid Atoms | |
Solvent Atoms | 112 |
Heterogen Atoms | 163 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |