2GA1
Crystal structure of a duf433 member protein (ava_0674) from anabaena variabilis atcc 29413 at 2.00 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP, NANODROP | 6.5 | 277 | 20.0% Glycerol, 0.16M Mg(oAc)2, 16.0% PEG-8000, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.8 | 50.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.98 | α = 90 |
b = 65.12 | β = 90 |
c = 86.86 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | 1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing | 2006-02-14 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL1-5 | 0.918381, 0.978489, 0.979094 | SSRL | BL1-5 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2 | 28.64 | 99.1 | 0.056 | 8.86 | 3.549 | 18535 | 32.644 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2 | 2.07 | 97.3 | 0.342 | 2.33 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 2 | 28.64 | 18491 | 958 | 99.32 | 0.178 | 0.176 | 0.218 | RANDOM | 29.739 |
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] | |
2.03 | -0.7 | -1.33 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.498 |
r_dihedral_angle_4_deg | 16.942 |
r_dihedral_angle_3_deg | 12.846 |
r_scangle_it | 6.748 |
r_scbond_it | 5.097 |
r_dihedral_angle_1_deg | 4.889 |
r_mcangle_it | 2.995 |
r_mcbond_it | 2.256 |
r_angle_refined_deg | 1.485 |
r_angle_other_deg | 0.852 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1588 |
Nucleic Acid Atoms | |
Solvent Atoms | 200 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
SOLVE | phasing |