3JZD
Crystal structure of Putative alcohol dehedrogenase (YP_298327.1) from RALSTONIA EUTROPHA JMP134 at 2.10 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | 0.1900M CaCl2, 5.0000% Glycerol, 26.6000% PEG-400, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.35 | 63.33 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 143.841 | α = 90 |
b = 143.841 | β = 90 |
c = 169.011 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
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 | MARMOSAIC 325 mm CCD | Flat mirror (vertical focusing) | 2009-02-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | SSRL | BL11-1 |
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 | 2.1 | 29.709 | 99.5 | 0.123 | 8.98 | 117762 | -3 | 27.926 |
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 | 2.1 | 2.17 | 99.3 | 0.83 | 1.5 |
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 | SAD | THROUGHOUT | 2.1 | 29.709 | 117704 | 5902 | 99.89 | 0.176 | 0.174 | 0.21 | RANDOM | 24.674 |
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] | |
0.49 | 0.24 | 0.49 | -0.73 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 26.772 |
r_dihedral_angle_4_deg | 14.938 |
r_dihedral_angle_3_deg | 12.208 |
r_scangle_it | 6.435 |
r_scbond_it | 4.478 |
r_dihedral_angle_1_deg | 3.418 |
r_mcangle_it | 2.257 |
r_angle_refined_deg | 1.652 |
r_mcbond_it | 1.213 |
r_angle_other_deg | 0.983 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10282 |
Nucleic Acid Atoms | |
Solvent Atoms | 878 |
Heterogen Atoms | 295 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
SHELX | phasing |
MolProbity | model building |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
SHELXD | phasing |
autoSHARP | phasing |