1MB4
Crystal structure of aspartate semialdehyde dehydrogenase from vibrio cholerae with NADP and S-methyl-l-cysteine sulfoxide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GL3 | PDB ENTRY 1GL3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 293 | 20% PEG 3350, 0.2M Sodium Acetate, 0.1M Sodium citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.74 | 55.14 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 107.63 | ¦Á = 90 |
b = 107.63 | ¦Â = 90 |
c = 153.538 | ¦Ã = 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 | 90 | CCD | ADSC QUANTUM 4 | 2001-09-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-BM-C | 1.000 | APS | 14-BM-C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.84 | 62.5 | 99.5 | 0.084 | 0.084 | 19.4 | 12.2 | 76343 | 1 | 1 | 16.8 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.84 | 1.91 | 95.4 | 0.34 | 0.34 | 3.59 | 10.45 | 14265 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1GL3 | 1.84 | 62.5 | 78132 | 76343 | 6053 | 97.6 | 0.192 | 0.192 | 0.229 | RANDOM | 23.3 |
Temperature Factor Modeling | ||||||
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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 | 0.05 | -0.1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.2 |
c_scangle_it | 3.07 |
c_scbond_it | 2.03 |
c_mcangle_it | 1.69 |
c_angle_deg | 1.4 |
c_mcbond_it | 1.04 |
c_improper_angle_d | 0.86 |
c_bond_d | 0.007 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5654 |
Nucleic Acid Atoms | |
Solvent Atoms | 457 |
Heterogen Atoms | 110 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SCALEPACK | data scaling |
CNS | refinement |
HKL-2000 | data reduction |
CNS | phasing |