2C57

H.pylori type II dehydroquinase in complex with FA1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.810MG/ML PROTEIN AGAINST 30% 1,4 BUTANDIOL, 0.1M SODIUM ACETATE PH 4.5 USING SITTING DROP METHOD
Crystal Properties
Matthews coefficientSolvent content
3.3763.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.863α = 90
b = 103.863β = 90
c = 217.531γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2002-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.5SRSPX9.5

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
13.0846.690.40.09104.54378178
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)
13.13.1581.60.851.23

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 2C4W3.12535869396883.80.210.2070.237RANDOM61.18
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]
1.050.521.05-1.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.766
r_dihedral_angle_3_deg20.972
r_dihedral_angle_4_deg8.844
r_dihedral_angle_1_deg7.733
r_angle_refined_deg2.076
r_scangle_it0.786
r_scbond_it0.611
r_symmetry_hbond_refined0.529
r_mcangle_it0.421
r_nbtor_refined0.338
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.766
r_dihedral_angle_3_deg20.972
r_dihedral_angle_4_deg8.844
r_dihedral_angle_1_deg7.733
r_angle_refined_deg2.076
r_scangle_it0.786
r_scbond_it0.611
r_symmetry_hbond_refined0.529
r_mcangle_it0.421
r_nbtor_refined0.338
r_mcbond_it0.317
r_nbd_refined0.264
r_symmetry_vdw_refined0.234
r_xyhbond_nbd_refined0.183
r_chiral_restr0.125
r_bond_refined_d0.024
r_gen_planes_refined0.007
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_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 Atoms14224
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing