2HK9
Crystal structure of shikimate dehydrogenase from aquifex aeolicus in complex with shikimate and NADP+ at 2.2 angstrom resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2HK7 | PDB ENTRY 2HK7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.2 | 292 | 30% w/v PEG4K in 0.1M sodium acetate (pH 4.6), pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.24 | 45.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 71.999 | α = 90 |
b = 119.803 | β = 90 |
c = 128.872 | 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 | BRUKER PROTEUM 300 | 2005-11-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.000 | APS | 22-ID |
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 | 30 | 83.9 | 0.109 | 8.8 | 2.9 | 47970 | 47970 | 44.4 |
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) | |||||||||||
2.2 | 2.28 | 54.5 | 0.331 | 2.1 | 1.6 | 3070 |
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 2HK7 | 2.2 | 29.41 | 47090 | 47090 | 2364 | 82.3 | 0.207 | 0.207 | 0.271 | RANDOM | 50.1 |
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] | |
-13.61 | 9.8 | 3.81 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.7 |
c_scangle_it | 8.26 |
c_scbond_it | 6.16 |
c_mcangle_it | 5.4 |
c_mcbond_it | 3.94 |
c_angle_deg | 1.3 |
c_improper_angle_d | 0.92 |
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 | 8447 |
Nucleic Acid Atoms | |
Solvent Atoms | 204 |
Heterogen Atoms | 223 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
MAR345 | data collection |
PHASER | phasing |