3FD3
Structure of the C-terminal domains of a LysR family protein from Agrobacterium tumefaciens str. C58.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 5.6 | 295 | 0.1M sodium citrate pH5.6, 0.1M ammonium acetate, 15% PEG 4000, 1/800 (w/w) endoproteinase Glu-C V8, VAPOR DIFFUSION, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.99 | 58.84 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.613 | α = 90 |
b = 53.613 | β = 90 |
c = 188.027 | γ = 90 |
Symmetry | |
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Space Group | P 43 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 | 2008-08-07 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97935,0.97948 | APS | 19-ID |
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 | 1.7 | 50 | 98.3 | 0.074 | 51 | 14.8 | 30842 | 30842 | -3 | 25.6 |
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 | 1.7 | 1.73 | 78.4 | 0.405 | 10.2 | 1235 |
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 | MAD | THROUGHOUT | 1.7 | 37.16 | 30737 | 30737 | 1550 | 98.2 | 0.171 | 0.171 | 0.169 | 0.2 | RANDOM | 26.747 |
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] | |
1.49 | 1.49 | -2.97 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.188 |
r_dihedral_angle_4_deg | 21.629 |
r_dihedral_angle_3_deg | 12.793 |
r_dihedral_angle_1_deg | 5.874 |
r_scangle_it | 3.503 |
r_scbond_it | 2.234 |
r_mcangle_it | 1.389 |
r_angle_refined_deg | 1.381 |
r_angle_other_deg | 0.831 |
r_mcbond_it | 0.76 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1572 |
Nucleic Acid Atoms | |
Solvent Atoms | 236 |
Heterogen Atoms | 40 |
Software
Software | |
---|---|
Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
MLPHARE | phasing |
DM | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SBC-Collect | data collection |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
HKL-3000 | phasing |
SHELXD | phasing |
SHELXE | model building |
SOLVE | phasing |
RESOLVE | phasing |
ARP/wARP | model building |
CCP4 | phasing |
O | model building |
Coot | model building |