5HUB

High-resolution structure of chorismate mutase from Corynebacterium glutamicum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VKL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.6293100 mM NH4 formate, pH 6.6 100 mM KSCN 30% PEG 2000 MME
Crystal Properties
Matthews coefficientSolvent content
1.9336.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.858α = 90
b = 24.627β = 99.43
c = 38.546γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97908ESRFID29

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
11.0640.8787.90.0568.964.330562
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)
11.061.1349.21.9370.443

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 REPLACEMENTTHROUGHOUT2VKL1.0640.8729317155887.650.175480.173250.22021RANDOM20.591
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]
1.5-0.63-0.92-0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free32.189
r_dihedral_angle_2_deg24.84
r_dihedral_angle_4_deg20.121
r_sphericity_bonded15.208
r_dihedral_angle_3_deg15.086
r_dihedral_angle_1_deg4.697
r_long_range_B_refined3.711
r_rigid_bond_restr3.706
r_long_range_B_other3.254
r_scangle_other2.477
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free32.189
r_dihedral_angle_2_deg24.84
r_dihedral_angle_4_deg20.121
r_sphericity_bonded15.208
r_dihedral_angle_3_deg15.086
r_dihedral_angle_1_deg4.697
r_long_range_B_refined3.711
r_rigid_bond_restr3.706
r_long_range_B_other3.254
r_scangle_other2.477
r_mcangle_other2.258
r_mcangle_it2.208
r_scbond_it2.135
r_angle_refined_deg2.012
r_scbond_other2.007
r_mcbond_other1.789
r_mcbond_it1.763
r_angle_other_deg1.282
r_chiral_restr0.115
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_gen_planes_other0.004
r_bond_other_d0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms629
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
XDSdata scaling