1VLL
Crystal structure of alanine dehydrogenase (AF1665) from Archaeoglobus fulgidus at 2.80 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 293 | 0.05M Acetic Acid, 0.052M Citrate_Na3, 29% PEG MME 550 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K | |
2 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 293 | 0.05M Acetic Acid, 0.05M Citrate_Na3, 30% PEG MME 550 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.22 |
2.7 | 54.03 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.702 | α = 90 |
b = 92.437 | β = 90 |
c = 131.783 | 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 | 2004-02-04 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | ADSC | 2003-09-20 | M | MAD | ||||||
1,2 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | ALS | 8.3.1 | |
2 | SYNCHROTRON | ALS BEAMLINE 8.2.1 | 0.9794, 0.9796, 1.0000 | ALS | 8.2.1 |
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 | 2.8 | 56.7 | 99.9 | 0.057 | 14.8 | 3.7 | 17713 | 84.89 |
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 | 2.8 | 2.87 | 99.8 | 0.362 | 2.3 | 3.3 | 1280 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.8 | 52.09 | 16757 | 897 | 99.79 | 0.21926 | 0.21742 | 0.2539 | RANDOM | 49.558 |
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] | |
-1.6 | -1.47 | 3.08 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.526 |
r_dihedral_angle_3_deg | 17.346 |
r_dihedral_angle_4_deg | 16.672 |
r_scangle_it | 6.284 |
r_dihedral_angle_1_deg | 5.836 |
r_scbond_it | 4.204 |
r_mcangle_it | 2.049 |
r_angle_refined_deg | 1.312 |
r_mcbond_it | 1.184 |
r_nbtor_refined | 0.308 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4574 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
SOLVE | phasing |
RESOLVE | model building |
REFMAC | refinement |
CCP4 | data scaling |
RESOLVE | phasing |