6BI4

2.9 Angstrom Resolution Crystal Structure of dTDP-Glucose 4,6-dehydratase (rfbB) from Bacillus anthracis str. Ames in Complex with NAD.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R66 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8295PROTEIN: TOTAL RFBB AND RFBC AT 7.5 MG/ML IN 10 MM TRIS HCL PH 8.3, 500 MM NACL, 5 MM BME, 10% GLYCEROL, 5 MM MGCL2, AND 1 MM NAD+. SCREEN: 0.1 M TRIS HCL PH 8.0, 1.56 M AMMONIUM SULFATE, AND 8.5% (W/V) PEG3350. CRYO-PROTECTANT SOLUTION: 1:1 RATIO OF 3.6 M AMMONIUM SULFATE AND 50% SUCROSE.
Crystal Properties
Matthews coefficientSolvent content
3.1460.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 165.557α = 90
b = 165.557β = 90
c = 292.121γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2012-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.93099.90.150.150.1580.051139.444858-369.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.92.951000.7710.7710.8130.2560.8432.99.7

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 REPLACEMENTTHROUGHOUT1R662.9129.9542594226499.730.169280.167420.20436RANDOM66.28
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]
-3.8-3.87.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.624
r_dihedral_angle_4_deg15.03
r_dihedral_angle_3_deg11.72
r_dihedral_angle_1_deg2.864
r_angle_refined_deg1.667
r_angle_other_deg1.007
r_chiral_restr0.116
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.624
r_dihedral_angle_4_deg15.03
r_dihedral_angle_3_deg11.72
r_dihedral_angle_1_deg2.864
r_angle_refined_deg1.667
r_angle_other_deg1.007
r_chiral_restr0.116
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.005
r_gen_planes_other0.005
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms10012
Nucleic Acid Atoms
Solvent Atoms76
Heterogen Atoms294

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing