1H0R

Type II Dehydroquinase from Mycobacterium tuberculosis complexed with 2,3-anhydro-quinic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DHQPDB ENTRY 2DHQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.515% PEG 8K, 0.2M NA/K PHOSPHATE 0.1M TRIS, pH 8.50
Crystal Properties
Matthews coefficientSolvent content
2.7755.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.879α = 90
b = 126.879β = 90
c = 126.879γ = 90
Symmetry
Space GroupF 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD1999-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.6SRSPX9.6

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.17099.50.1119.64.443406
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1499.50.7421.754.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2DHQ2.172.55837490192.80.1440.216RANDOM17.88
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.244
r_scangle_it4.861
r_scbond_it3.181
r_angle_other_deg2.944
r_mcangle_it2.215
r_angle_refined_deg2.191
r_mcbond_it1.32
r_nbd_refined0.406
r_symmetry_vdw_other0.298
r_nbd_other0.254
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.244
r_scangle_it4.861
r_scbond_it3.181
r_angle_other_deg2.944
r_mcangle_it2.215
r_angle_refined_deg2.191
r_mcbond_it1.32
r_nbd_refined0.406
r_symmetry_vdw_other0.298
r_nbd_other0.254
r_symmetry_vdw_refined0.208
r_xyhbond_nbd_refined0.198
r_symmetry_hbond_refined0.161
r_chiral_restr0.144
r_nbtor_other0.092
r_bond_refined_d0.026
r_gen_planes_other0.016
r_gen_planes_refined0.013
r_bond_other_d0.004
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1048
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing