5LKW

Crystal structure of the peptidoglycan-associated lipoprotein (Pal) from Burkholderia cepacia in complex with DAP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4B5C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52930.1M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3350, 10mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.2645.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.706α = 90
b = 77.706β = 90
c = 38.606γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442015-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

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
12301000.0844.95.516690
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)
122.0382.30.4381.63.1

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 REPLACEMENTTHROUGHOUT4B5C214.691507380190.320.191380.188310.24909RANDOM29.4
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]
-0.01-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.189
r_dihedral_angle_4_deg17.856
r_dihedral_angle_3_deg17.234
r_dihedral_angle_1_deg6.818
r_scangle_it5.101
r_scbond_it3.2
r_mcangle_it1.874
r_angle_refined_deg1.847
r_mcbond_it1.076
r_chiral_restr0.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.189
r_dihedral_angle_4_deg17.856
r_dihedral_angle_3_deg17.234
r_dihedral_angle_1_deg6.818
r_scangle_it5.101
r_scbond_it3.2
r_mcangle_it1.874
r_angle_refined_deg1.847
r_mcbond_it1.076
r_chiral_restr0.122
r_bond_refined_d0.021
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
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_other
r_mcangle_other
r_scbond_other
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 Atoms1904
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms18

Software

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