3B2N
Crystal structure of DNA-binding response regulator, LuxR family, from Staphylococcus aureus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 294 | 0.1 M Hepes pH 7.5, 1.4 M Sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.42 | 49.21 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 67.898 | α = 90 |
b = 67.898 | β = 90 |
c = 110.662 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 61 2 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 | X29 | 2007-10-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 0.97900 | NSLS | X29A |
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 | 2.04 | 50 | 86.5 | 0.083 | 10.2 | 6.4 | 15739 |
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 | 2.04 | 2.11 | 22.9 | 0.436 | 1.6 | 416 |
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 | SAD | THROUGHOUT | 2.04 | 20 | 9087 | 436 | 89.86 | 0.168 | 0.165 | 0.215 | RANDOM | 38.829 |
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] | |
0.06 | 0.03 | 0.06 | -0.09 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.77 |
r_dihedral_angle_4_deg | 19.578 |
r_dihedral_angle_3_deg | 17.342 |
r_scbond_it | 11.587 |
r_dihedral_angle_1_deg | 6.49 |
r_scangle_it | 6.446 |
r_mcangle_it | 5.504 |
r_angle_refined_deg | 1.661 |
r_mcbond_it | 1.555 |
r_symmetry_hbond_refined | 0.386 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 955 |
Nucleic Acid Atoms | |
Solvent Atoms | 57 |
Heterogen Atoms | 1 |
Software
Software | |
---|---|
Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
SHELX | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CBASS | data collection |
SHELXD | phasing |