3SZ8
Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia pseudomallei
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 290 | EBS internal tracking number 223672H7. PACT H7. 0.2 M Na acetate, 0.1 M Bis Tris propane pH 8.5, 20% PEG 3350. BupsA.00102.a.A1 PS00621 at 30.3 mg/mL, vapor diffusion, sitting drop, temperature 290K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.32 | 47.05 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 85.49 | α = 90 |
b = 83.32 | β = 116.59 |
c = 87.87 | 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 | 100 | CCD | MARMOSAIC 300 mm CCD | 2011-06-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 1.03317 | APS | 23-ID-D |
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 | 2.05 | 50 | 99.2 | 0.067 | 13.62 | 3.6 | 68845 | -3 | 33.651 |
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 | 2.05 | 2.1 | 99.1 | 0.47 | 2.6 | 3.4 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.05 | 43.81 | 68771 | 3483 | 99.29 | 0.185 | 0.183 | 0.221 | RANDOM | 26.294 |
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] | |
0.34 | 0.9 | 0.22 | 0.25 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.004 |
r_dihedral_angle_4_deg | 15.22 |
r_dihedral_angle_3_deg | 13.085 |
r_dihedral_angle_1_deg | 5.765 |
r_scangle_it | 3.62 |
r_scbond_it | 2.176 |
r_angle_refined_deg | 1.417 |
r_mcangle_it | 1.324 |
r_angle_other_deg | 0.933 |
r_mcbond_it | 0.722 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 7789 |
Nucleic Acid Atoms | |
Solvent Atoms | 555 |
Heterogen Atoms | 16 |
Software
Software | |
---|---|
Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |