5J6F

Crystal structure of DAH7PS-CM complex from Geobacillus sp. with prephenate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3TFC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION6.5298A protein solution (11 mg/mL in 20 mM BTP, 40 mM KCl, 200 ??M PEP, pH 7.4) was mixed 1:1 (v/v) with a reservoir solution containing 0.2 M sodium citrate, 0.1 M BTP, pH 6.5, 20% W/V PEG 3350 and 0.2 mM chorismic acid. 2 ??L drop size. 500 ??L reservoir volume.
Crystal Properties
Matthews coefficientSolvent content
2.6653.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.438α = 90
b = 95.438β = 90
c = 167.452γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315r2012-04-19MSINGLE 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
12.7582.6599.90.0791187.622482
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)
12.752.881001.3367.7

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 REPLACEMENTTHROUGHOUT3TFC2.7582.6521178105499.020.184710.182210.2352RANDOM77.759
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]
-0.49-0.24-0.491.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.677
r_dihedral_angle_3_deg18.841
r_dihedral_angle_4_deg16.568
r_long_range_B_other7.983
r_long_range_B_refined7.981
r_dihedral_angle_1_deg6.922
r_scangle_other6.26
r_mcangle_it4.289
r_mcangle_other4.289
r_scbond_it3.895
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.677
r_dihedral_angle_3_deg18.841
r_dihedral_angle_4_deg16.568
r_long_range_B_other7.983
r_long_range_B_refined7.981
r_dihedral_angle_1_deg6.922
r_scangle_other6.26
r_mcangle_it4.289
r_mcangle_other4.289
r_scbond_it3.895
r_scbond_other3.894
r_mcbond_it2.729
r_mcbond_other2.726
r_angle_refined_deg2.12
r_angle_other_deg1.511
r_chiral_restr0.107
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.007
r_gen_planes_other0.007
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 Atoms5366
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction