3UDU
Crystal structure of putative 3-isopropylmalate dehydrogenase from Campylobacter jejuni
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1CM7 | PDB ENTRY 1CM7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 297 | 25%PEG3350, 0.2M Na Chloride, 0.1MHEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.39 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.717 | α = 94.19 |
b = 83.17 | β = 90.07 |
c = 111.204 | γ = 89.64 |
Symmetry | |
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Space Group | P 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 | ADSC QUANTUM 315r | 2010-03-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.9793 | APS | 19-ID |
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 | 1.85 | 50 | 99.7 | 0.093 | 0.093 | 18.2 | 2.5 | 213853 | 213853 | -3 | 30.7 |
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 | 1.85 | 1.88 | 94.7 | 0.554 | 0.554 | 2 | 2.5 | 10781 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MIR | THROUGHOUT | PDB ENTRY 1CM7 | 1.85 | 50 | 205131 | 205131 | 10935 | 94.72 | 0.19951 | 0.19951 | 0.19749 | 0.23639 | RANDOM | 24.991 |
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] | |
-0.62 | 0.18 | 0.25 | -2.97 | -0.13 | 3.57 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.252 |
r_dihedral_angle_4_deg | 14.41 |
r_dihedral_angle_3_deg | 13.133 |
r_dihedral_angle_1_deg | 6.004 |
r_angle_other_deg | 4.332 |
r_angle_refined_deg | 1.817 |
r_chiral_restr | 0.112 |
r_bond_refined_d | 0.019 |
r_gen_planes_other | 0.014 |
r_gen_planes_refined | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 21851 |
Nucleic Acid Atoms | |
Solvent Atoms | 1816 |
Heterogen Atoms | 25 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data collection |
HKL-3000 | phasing |
SHELXD | phasing |
SHELXE | model building |
DM | model building |
MLPHARE | phasing |
RESOLVE | model building |
CCP4 | model building |
ARP/wARP | model building |
REFMAC | refinement |
Coot | model building |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
DM | phasing |
RESOLVE | phasing |
CCP4 | phasing |