2O8Q
CRYSTAL STRUCTURE OF A PROTEIN WITH A CUPIN-LIKE FOLD AND UNKNOWN FUNCTION (BXE_C0505) FROM BURKHOLDERIA XENOVORANS LB400 AT 1.55 A RESOLUTION
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP, NANODROP | 9 | 277 | 2.0% Dioxane, 10.0% PEG-20000, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
2 | VAPOR DIFFUSION, SITTING DROP, NANODROP | 6.6 | 277 | 0.2M (NH4)2Tartrate, 20.0% PEG-3350, No Buffer pH 6.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 102.255 | α = 90 |
b = 102.255 | β = 90 |
c = 74.746 | γ = 90 |
Symmetry | |
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Space Group | P 42 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 | ADSC QUANTUM 315 | 1m long Rh coated bent cylindrical mirror forhorizontal and vertical focussing | 2006-11-17 | M | SINGLE WAVELENGTH | |||||
2 | 2 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | Adjustable focusing mirrors in K-B geometry | 2006-10-20 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL1-5 | SSRL | BL1-5 | |
2 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 0.97921, 0.97888, 0.94645 | APS | 23-ID-D |
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 | 1.55 | 29.683 | 100 | 0.067 | 0.067 | 7.5 | 9.1 | 57924 | 21.35 |
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) | ||||||||||
1,2 | 1.55 | 1.59 | 99.7 | 0.965 | 0.965 | 0.8 | 7 | 4157 |
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 | 1.55 | 29.683 | 57868 | 2939 | 99.95 | 0.171 | 0.17 | 0.191 | RANDOM | 20.305 |
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] | |
-0.03 | -0.03 | 0.05 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.541 |
r_dihedral_angle_4_deg | 19.63 |
r_dihedral_angle_3_deg | 12.652 |
r_dihedral_angle_1_deg | 9.118 |
r_scangle_it | 6.464 |
r_scbond_it | 4.504 |
r_mcangle_it | 3.183 |
r_mcbond_it | 2.062 |
r_angle_refined_deg | 1.837 |
r_angle_other_deg | 1.006 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1900 |
Nucleic Acid Atoms | |
Solvent Atoms | 231 |
Heterogen Atoms | 34 |
Software
Software | |
---|---|
Software Name | Purpose |
MolProbity | model building |
SHELX | phasing |
REFMAC | refinement |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
CCP4 | data scaling |
SHELXD | phasing |
SOLVE | phasing |