4PX7

Crystal structure of lipid phosphatase E. coli PgpB


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.528920mM CaCl2, 10mM MgSO4, 20mM MES (pH 6.5), 7.7% (w/v) polyethylene glycol 1500, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.9357.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.715α = 90
b = 73.667β = 90
c = 131.2γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200PIXELDECTRIS PILATUS 6M2013-10-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-1A0.9788Photon FactoryBL-1A

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
13.232.86990.12911.86362629933
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)
13.23.3190.50.7173.710.5565

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSAD3.232.861.89625651098.980.27150.27150.270.3023RANDOM
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_d17.54
f_angle_d1.258
f_chiral_restr0.082
f_plane_restr0.007
f_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1921
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms22

Software

Software
Software NamePurpose
HKL-2000data collection
SOLVEphasing
PHENIXrefinement
DENZOdata reduction
SCALAdata scaling