2Q7U
Crystal Structure of the F plasmid TraI Relaxase Domain with the Scissile Thymidine Base and Imidodiphosphate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | protein buffer: 50 mM NaCl, 10% glycerol, 10 mM Tris-HCl pH 7.5, mother liquor: 75 mM sodium nitrate, 14% w/v PEG 3350, 10 mM spermine, 110 uM oriT DNA soaked (24 hours): 200 mM ammonium nitrate, 40% w/v PEG 3350, and 1 mM N,N-imidobisphosphonate (PNP), VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
1.84 | 33.2 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 44.5 | α = 90 |
b = 86.31 | β = 90 |
c = 127.91 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 21 |
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 | 2006-02-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 0.97173 | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 3 | 50 | 92.8 | 0.135 | 8.6 | 4.1 | 11257 | 10447 | 23 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
3 | 3.11 | 72.7 | 0.382 | 3.9 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1p4d | 3 | 38.23 | 11257 | 9059 | 941 | 87.1 | 0.215 | 0.215 | 0.214 | 0.312 | RANDOM | 38.6 |
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] | |
-5.48 | 32.74 | -27.26 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.5 |
c_scangle_it | 4.42 |
c_scbond_it | 2.68 |
c_mcangle_it | 2.49 |
c_mcbond_it | 1.4 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.82 |
c_bond_d | 0.008 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4132 |
Nucleic Acid Atoms | |
Solvent Atoms | 45 |
Heterogen Atoms | 26 |
Software
Software | |
---|---|
Software Name | Purpose |
CNS | refinement |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |