2NQW
Structure of the transporter associated domain from PG_0272, a CBS domain protein from Porphyromonas gingivalis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 3.5 | 291 | 0.1M citric acid, 25% PEG 3350, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.03 | 39.48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 33.733 | α = 90 |
b = 45.195 | β = 90 |
c = 57.214 | γ = 90 |
Symmetry | |
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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-MADE | 2006-10-29 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.97910, 0.97929 | APS | 19-BM |
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 | 1.3 | 24.2 | 94.6 | 0.068 | 11.6 | 7.8 | 20972 | 20972 | -3 | 16.11 |
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) | |||||||||||
1 | 1.3 | 1.33 | 69 | 0.264 | 3.6 | 3.6 |
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 | 1.3 | 24.17 | 19898 | 19898 | 1072 | 94.63 | 0.13157 | 0.13157 | 0.12978 | 0.16715 | RANDOM | 15.998 |
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] | |
1.31 | -0.71 | -0.6 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.537 |
r_dihedral_angle_3_deg | 10.925 |
r_dihedral_angle_4_deg | 10.869 |
r_sphericity_free | 7.207 |
r_dihedral_angle_1_deg | 6.415 |
r_scangle_it | 4.834 |
r_sphericity_bonded | 4.655 |
r_scbond_it | 3.381 |
r_mcangle_it | 2.196 |
r_rigid_bond_restr | 2.022 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 709 |
Nucleic Acid Atoms | |
Solvent Atoms | 185 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SBC-Collect | data collection |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
HKL-3000 | phasing |
SHELXD | phasing |
SHELXE | model building |
MLPHARE | phasing |
DM | phasing |
SOLVE | phasing |
RESOLVE | phasing |
ARP/wARP | model building |
CCP4 | phasing |
O | model building |
Coot | model building |