3N59

Type II dehydroquinase from Mycobacterium Tuberculosis complexed with 3-dehydroshikimate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH290MtDHQase 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
Matthews coefficientSolvent content
2.1943.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.988α = 90
b = 137.334β = 95.98
c = 148.101γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97856APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.515095.11124512124512-3-3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2dhq2.5250118244626795.130.200080.197540.24779RANDOM37.126
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]
0.120.880.32-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.675
r_dihedral_angle_3_deg13.862
r_dihedral_angle_4_deg10.386
r_dihedral_angle_1_deg4.559
r_angle_refined_deg0.882
r_scangle_it0.518
r_mcangle_it0.366
r_scbond_it0.299
r_nbtor_refined0.29
r_mcbond_it0.204
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.675
r_dihedral_angle_3_deg13.862
r_dihedral_angle_4_deg10.386
r_dihedral_angle_1_deg4.559
r_angle_refined_deg0.882
r_scangle_it0.518
r_mcangle_it0.366
r_scbond_it0.299
r_nbtor_refined0.29
r_mcbond_it0.204
r_symmetry_vdw_refined0.19
r_nbd_refined0.159
r_xyhbond_nbd_refined0.088
r_symmetry_hbond_refined0.088
r_chiral_restr0.053
r_bond_refined_d0.005
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms24621
Nucleic Acid Atoms
Solvent Atoms1604
Heterogen Atoms48

Software

Software
Software NamePurpose
HKL-3000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling