4GHJ
1.75 Angstrom Crystal Structure of Transcriptional Regulator ftom Vibrio vulnificus.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 9 | 295 | Protein: 7.6mg/mL, 0.5M Sodium cloride, 0.01M Tris-HCl pH 8.3; Screen: PACT (D6), 0.1M MMT buffer pH 9.0, 25% (w/v) PEG 1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
1.76 | 29.99 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 63.742 | α = 90 |
b = 70.74 | β = 90 |
c = 35.746 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 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 300 mm CCD | Beryllium lenses | 2012-07-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
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 | 30 | 97.6 | 0.095 | 31.3 | 6.9 | 16622 | 16622 | -3 | 21.7 |
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 | 1.75 | 1.78 | 83.6 | 0.482 | 3.3 | 5.8 | 713 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.75 | 28.53 | 15662 | 15662 | 847 | 97.5 | 0.18366 | 0.18366 | 0.18157 | 0.22341 | RANDOM | 21.626 |
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] | |
-2.88 | 4.4 | -1.52 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.073 |
r_dihedral_angle_4_deg | 12.816 |
r_dihedral_angle_3_deg | 9.897 |
r_scangle_it | 5.193 |
r_scbond_it | 3.176 |
r_dihedral_angle_1_deg | 2.887 |
r_mcangle_it | 1.904 |
r_angle_refined_deg | 1.227 |
r_mcbond_it | 1.158 |
r_angle_other_deg | 0.811 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1148 |
Nucleic Acid Atoms | |
Solvent Atoms | 149 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
Blu-Ice | data collection |
PHENIX | model building |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHENIX | phasing |