6AL9

Crystal structure of chorismate mutase from Helicobacter pylori in complex with prephenate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YBZ1YBZ, 2D8D and 3RMI
experimental modelPDB 2D8D1YBZ, 2D8D and 3RMI
experimental modelPDB 3RMI1YBZ, 2D8D and 3RMI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293.150.1 M MES pH 6.5, 0.2 M ammonium acetate, 35% glycerol ethoxylate, 0.5 mM chorismate acid
Crystal Properties
Matthews coefficientSolvent content
2.2745.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.869α = 90
b = 63.526β = 90
c = 166.918γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-03-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.953700Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.241.7399.10.1210.99611.68.910877
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.212.2899.80.3720.9114.18.6

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 REPLACEMENTTHROUGHOUT1YBZ, 2D8D and 3RMI2.319.43909746499.730.20760.206110.23691RANDOM38.789
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]
-0.230.55-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.246
r_dihedral_angle_4_deg26.401
r_dihedral_angle_3_deg19.034
r_long_range_B_refined7.394
r_long_range_B_other7.392
r_dihedral_angle_1_deg6.368
r_scangle_other5.569
r_mcangle_it3.894
r_mcangle_other3.892
r_scbond_it3.412
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.246
r_dihedral_angle_4_deg26.401
r_dihedral_angle_3_deg19.034
r_long_range_B_refined7.394
r_long_range_B_other7.392
r_dihedral_angle_1_deg6.368
r_scangle_other5.569
r_mcangle_it3.894
r_mcangle_other3.892
r_scbond_it3.412
r_angle_other_deg3.41
r_scbond_other3.41
r_mcbond_other2.523
r_mcbond_it2.522
r_angle_refined_deg1.301
r_chiral_restr0.329
r_bond_refined_d0.01
r_gen_planes_other0.006
r_gen_planes_refined0.005
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1488
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing