2V84
Crystal Structure of the Tp0655 (TpPotD) Lipoprotein of Treponema pallidum
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | CRYSTALS WERE GROWN AT 20 DEGRRES C USING THE VAPOR DIFFUSION METHOD IN HANGING DROP MODE BY MIXING 1 MICROLITER PROTEIN (20 MG/ML) IN 20 MM HEPES, PH 7.0, 0.1 M NACL, 2 MM BETA-OCTYL GLUCOSIDE WITH 1 MICROLITER RESERVOIR SOLUTION (10-12% (W/V) PEG 20K, 0.1 M MES, PH 6.5) AND EQUILIBRATING AGAINST 1 ML OF RESERVOIR SOLUTION. CRYSTALS APPEARED WITHIN SEVERAL HOURS AND GREW TO A FINAL SIZE OF 0.2 X 0.2 X 0.8 MM IN ABOUT 2 DAYS. THE CRYSTALS WERE CRYO-PROTECTED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 20% (V/V) ETHYLENE GLYCOL, AND THEN FLASH-COOLED IN LIQUID NITROGEN. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.5 | 52 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 51.61 | α = 90 |
b = 86.27 | β = 90 |
c = 89.5 | 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 | CUSTOM | 2007-02-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | APS | 19-BM |
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 | 1.78 | 31.04 | 99.7 | 0.05 | 39.4 | 6.7 | 39206 | -3 | 29.6 |
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 | 1.78 | 1.8 | 97.2 | 0.83 | 2 | 4.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | NONE | 1.78 | 30 | 35504 | 1893 | 95.3 | 0.236 | 0.234 | 0.26 | RANDOM | 32.7 |
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] | |
0.17 | -0.53 | 0.36 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.754 |
r_dihedral_angle_3_deg | 15.491 |
r_dihedral_angle_4_deg | 14.178 |
r_dihedral_angle_1_deg | 5.638 |
r_scangle_it | 2.415 |
r_scbond_it | 1.658 |
r_angle_refined_deg | 1.289 |
r_mcangle_it | 1.075 |
r_mcbond_it | 0.645 |
r_nbtor_refined | 0.312 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2575 |
Nucleic Acid Atoms | |
Solvent Atoms | 128 |
Heterogen Atoms | 29 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
HKL-3000 | phasing |