5VAT

Haemophilus influenzae LpoA: Monoclinic form (Mon2) with 2 molecules per a.u.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CKM3CKM, 4P29
experimental modelPDB 4P293CKM, 4P29

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP295One microliter of concentrated protein (33 mg/ml in 150 mm NaCl, 50 mm Tris-HCl, ph 8.0) and one microliter precipitant (8% polyethylene glycol 4000, 0.1 m sodium acetate trihydrate, ph 4.6) and 0.2 microliter 30% xylitol. Cryoprotectant: precipitant solution containing 15% glycerol.
Crystal Properties
Matthews coefficientSolvent content
3.1160.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.935α = 90
b = 72.695β = 94.42
c = 120.572γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray125CCDRAYONIX MX-300MONOCHROMATOR2009-10-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.07806APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.4910087.090.0870.1070.0610.911.92.664573639.5642078485
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.492.5365.10.5130.6470.3890.6352.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3CKM, 4P292.642.3411.3572309315381.820.22470.22330.256873.3186
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d9.132
f_angle_d0.542
f_chiral_restr0.039
f_plane_restr0.003
f_bond_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8410
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling