1YS4
Structure of Aspartate-Semialdehyde Dehydrogenase from Methanococcus jannaschii
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | 298 | sodium malonate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.00 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 95.254 | α = 90 |
b = 95.254 | β = 90 |
c = 297.957 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 4 | 2004-03-06 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 0.9743, 0.9797, 0.9796 | APS | 17-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.3 | 40 | 99.1 | 61981 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.3 | 2.38 | 98.7 |
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 | 2.29 | 39.22 | 58938 | 3145 | 99.2 | 0.193 | 0.191 | 0.221 | RANDOM | 36.36 |
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] | |
0.06 | 0.06 | -0.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
p_angle_d | 1.33 |
p_hb_or_metal_coord | 0.176 |
p_bond_d | 0.008 |
p_planar_d | 0.004 |
p_angle_deg | |
p_mcbond_it | |
p_mcangle_it | |
p_scbond_it | |
p_scangle_it | |
p_plane_restr |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5450 |
Nucleic Acid Atoms | |
Solvent Atoms | 429 |
Heterogen Atoms | 124 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
SHARP | phasing |