3N59
Type II dehydroquinase from Mycobacterium Tuberculosis complexed with 3-dehydroshikimate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2DHQ | PDB entry 2dhq |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 290 | MtDHQase protein was concentrated to 10-15 mg/mL prior to crystallization, using Amicon Ultra MWCO 5 KDa protein concentrators. MtDHQase crystals were grown in 4 uL drops composed of 5-7 mg/mL protein incubated with 1.5-fold M excess of ligand, 15% PEG monomethyl ether 2,000, 0.075 M KBr, 25 mM Tris, 50 mM NaCl, 0.5 mM DTT, 0.5 mM EDTA, pH 7.5 in microbatch plates covered with 5 mL Als oil, Microbatch, temperature 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.19 | 43.88 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 96.988 | α = 90 |
b = 137.334 | β = 95.98 |
c = 148.101 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 315 | 2007-11-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97856 | APS | 19-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 | 2.51 | 50 | 95.11 | 124512 | 124512 | -3 | -3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 2dhq | 2.52 | 50 | 118244 | 6267 | 95.13 | 0.20008 | 0.19754 | 0.24779 | RANDOM | 37.126 |
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] | |
0.12 | 0.88 | 0.32 | -0.26 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.675 |
r_dihedral_angle_3_deg | 13.862 |
r_dihedral_angle_4_deg | 10.386 |
r_dihedral_angle_1_deg | 4.559 |
r_angle_refined_deg | 0.882 |
r_scangle_it | 0.518 |
r_mcangle_it | 0.366 |
r_scbond_it | 0.299 |
r_nbtor_refined | 0.29 |
r_mcbond_it | 0.204 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 24621 |
Nucleic Acid Atoms | |
Solvent Atoms | 1604 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |