3TQD

Structure of the 3-deoxy-D-manno-octulosonate cytidylyltransferase (kdsB) from Coxiella burnetii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K8DPDB entry 3K8D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62980.17 M ammonium acetate, 0.085 M Na citrate, 25.5% PEG 4000, 15% glycerol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.244.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.752α = 90
b = 51.616β = 111.92
c = 78.874γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442011-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.810097.90.05339.49.92358223093-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.83880.4542.33.61186

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3K8D1.825.622366322946118496.970.190260.18820.22746RANDOM39.645
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]
0.230.272.06-2.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.052
r_dihedral_angle_4_deg15.824
r_dihedral_angle_3_deg14.428
r_dihedral_angle_1_deg6.181
r_scangle_it4.418
r_scbond_it2.781
r_mcangle_it1.747
r_angle_refined_deg1.653
r_mcbond_it1.018
r_angle_other_deg0.976
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.052
r_dihedral_angle_4_deg15.824
r_dihedral_angle_3_deg14.428
r_dihedral_angle_1_deg6.181
r_scangle_it4.418
r_scbond_it2.781
r_mcangle_it1.747
r_angle_refined_deg1.653
r_mcbond_it1.018
r_angle_other_deg0.976
r_mcbond_other0.301
r_chiral_restr0.101
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1921
Nucleic Acid Atoms
Solvent Atoms170
Heterogen Atoms5

Software

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