3D01
Crystal structure of the protein Atu1372 with unknown function from Agrobacterium tumefaciens
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 289 | 0.1M Bis-tris pH 5.5, 0.2M NH4(OAC), 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.25 | 62.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 93.623 | α = 68.2 |
b = 93.6 | β = 67.87 |
c = 93.628 | γ = 68.14 |
Symmetry | |
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Space Group | P 1 |
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 | Mirrors | 2006-12-04 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.9794, 0.9796 | 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 | 83.62 | 97 | 0.084 | 20.33 | 5 | 274501 | 266266 | 2 | 18.8 |
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 | 1.745 | 92.08 | 0.605 | 1.5 | 4 | 21313 |
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 | 46.13 | 266266 | 266266 | 14230 | 97 | 0.18066 | 0.18066 | 0.17888 | 0.21411 | RANDOM | 18.647 |
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] | |
-0.05 | -0.15 | -0.21 | 0.16 | -0.24 | 0.34 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.581 |
r_dihedral_angle_4_deg | 18.549 |
r_dihedral_angle_3_deg | 11.48 |
r_dihedral_angle_1_deg | 6.666 |
r_scangle_it | 5.446 |
r_scbond_it | 4.104 |
r_mcangle_it | 2.027 |
r_mcbond_it | 1.633 |
r_angle_refined_deg | 1.447 |
r_angle_other_deg | 0.925 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14016 |
Nucleic Acid Atoms | |
Solvent Atoms | 1074 |
Heterogen Atoms | 144 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SBC-Collect | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
HKL-3000 | phasing |