5HUD

Non-covalent complex of and DAHP synthase and chorismate mutase from Corynebacterium glutamicum with bound transition state analog


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2W1A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293100 mM imidazole/MES buffer, pH 6.5 30 mM each of ethylene glycol mix (di-ethylene glycol, tri-ethylene glycol, tetra-ethylene glycol, penta-ethylene glycol) 15% glycerol 15% PEG 4000 micro-seeded from badly diffracting crystals (approx. 8 AA resolution), in 100 mM Na-HEPES, pH 7.5, 200 mM LiSO4, 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.4564.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.622α = 90
b = 110.481β = 101.41
c = 134.652γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97239ESRFID29

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
12.1131.9996.70.1994.792.95190339
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)
12.12.2385.71.7630.442.24

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 REPLACEMENTTHROUGHOUT2W1A2.1540170847884697.990.251910.249520.298RANDOM33.789
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]
0.570.09-1.030.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.924
r_dihedral_angle_3_deg16.337
r_dihedral_angle_4_deg16.187
r_dihedral_angle_1_deg6.091
r_long_range_B_refined5.8
r_long_range_B_other5.8
r_scangle_other3.552
r_mcangle_it3.154
r_mcangle_other3.154
r_scbond_it2.165
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.924
r_dihedral_angle_3_deg16.337
r_dihedral_angle_4_deg16.187
r_dihedral_angle_1_deg6.091
r_long_range_B_refined5.8
r_long_range_B_other5.8
r_scangle_other3.552
r_mcangle_it3.154
r_mcangle_other3.154
r_scbond_it2.165
r_scbond_other2.165
r_mcbond_it1.926
r_mcbond_other1.926
r_angle_refined_deg1.531
r_angle_other_deg0.986
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms16558
Nucleic Acid Atoms
Solvent Atoms779
Heterogen Atoms871

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
Aimlessdata scaling
XDSdata scaling
XDSdata reduction