4BFC

Crystal structure of the C-terminal CMP-Kdo binding domain of WaaA from Acinetobacter baumannii


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
160.1M NA CITRATE BUFFER PH 6.0, 0.2 MM LITHIUM SULPHATE AND 17 TO 23 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.4664.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.37α = 90
b = 110.37β = 90
c = 70.34γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH MAR165MIRROR2012-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-3MAX III911-3

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
11.73099.40.0524.95.7350573.77
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)
11.71.898.80.463.775.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2XCI1.728.3333299175499.380.135180.133830.16093RANDOM29.23
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]
-9.83-9.8319.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.174
r_dihedral_angle_4_deg20.105
r_dihedral_angle_3_deg13.581
r_dihedral_angle_1_deg6.201
r_angle_refined_deg1.885
r_angle_other_deg1.885
r_chiral_restr0.135
r_bond_refined_d0.019
r_bond_other_d0.019
r_gen_planes_refined0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.174
r_dihedral_angle_4_deg20.105
r_dihedral_angle_3_deg13.581
r_dihedral_angle_1_deg6.201
r_angle_refined_deg1.885
r_angle_other_deg1.885
r_chiral_restr0.135
r_bond_refined_d0.019
r_bond_other_d0.019
r_gen_planes_refined0.011
r_gen_planes_other
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 Atoms1532
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing