2EGZ
Crystal structure of the 3-dehydroquinate dehydratase from Aquifex aeolicus VF5
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | LIQUID DIFFUSION | 5.6 | 291 | 30% PEG 4000, 0.2M Ammonium acetate, 0.1M Citrate pH5.6, LIQUID DIFFUSION, temperature 291K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.13 | 42.18 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 52.937 | α = 90 |
b = 67.614 | β = 99.2 |
c = 60.238 | γ = 90 |
Symmetry | |
---|---|
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 | 180 | CCD | RIGAKU JUPITER 210 | 2006-10-15 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B2 | 0.9788, 0.900, 0.9794 | SPring-8 | BL26B2 |
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 | 1.75 | 50 | 99.3 | 0.08 | 5.3 | 80554 | 2 | 2 | 13.1 |
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) | |||||||||||
1.75 | 1.81 | 94.4 | 0.287 | 4.3 | 3944 |
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 | 1.75 | 19.94 | 77918 | 2269 | 94.1 | 0.22 | 0.22 | 0.237 | RANDOM | 18.4 |
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] | |
3.78 | 2.66 | -3.22 | -0.56 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.2 |
c_scangle_it | 3.16 |
c_scbond_it | 2.12 |
c_mcangle_it | 1.75 |
c_angle_deg | 1.3 |
c_mcbond_it | 1.18 |
c_improper_angle_d | 0.81 |
c_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3442 |
Nucleic Acid Atoms | |
Solvent Atoms | 123 |
Heterogen Atoms | 20 |
Software
Software | |
---|---|
Software Name | Purpose |
CNS | refinement |
BSS | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
SOLVE | phasing |