6XOK

X-ray structure of the rhombohedral form of the lipase from Thermomyces lanuginosa at 1.3 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4EA6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5298Crystals were grown by vapor diffusion at room temperature in 24 well Cryschem sitting drop plates (Hampton Research, Aliso Viejo, CA) with 600 microleters reservoirs of 25% PEG 3350 in 0.10 M MES buffer at pH 6.5. The protein droplets were of 8ul volume and consisted of equal parts of a 20 to 30 mg/ml protein stock solution and the reservoir solution. Crystals usually appeared and grew to full size within one to two weeks. Rhombohedral crystals were thin needles of indeterminate cross-section
Crystal Properties
Matthews coefficientSolvent content
2.1342.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.373α = 90
b = 76.373β = 90
c = 241.551γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray173PIXELDECTRIS PILATUS3 X CdTe 1M2019-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.03ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.380880.0490.0490.050.008142.7315835819.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.3314.40.360.360.4610.2050.812.64.2

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-VALUE4EA61.3801.3758353286587.920.10560.10410.134321.44
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_d20.1
f_angle_d1.2443
f_chiral_restr0.0991
f_bond_d0.0079
f_plane_restr0.0072
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2015
Nucleic Acid Atoms
Solvent Atoms427
Heterogen Atoms108

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing