3QH4

Crystal structure of esterase LipW from Mycobacterium marinum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LZKpdb entry 1lzk

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8289protein at 55.6 mg/mL, 0.2 M MgCl2, 0.1 M Tris, 20 % PEG 6000, cryo-protected with 25 % ethylene glycol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289 K
Crystal Properties
Matthews coefficientSolvent content
2.1843.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.27α = 90
b = 86.99β = 90
c = 46.19γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2011-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
11.755098.90.03821.763.23051330172-317.905
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)
11.751.8950.0739.131.92212

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 1lzk1.755030076151598.560.14660.14450.1877RANDOM11.4448
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]
-0.170.45-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.432
r_dihedral_angle_4_deg18.718
r_dihedral_angle_3_deg11.076
r_dihedral_angle_1_deg5.577
r_scangle_it3.308
r_scbond_it2.101
r_angle_refined_deg1.4
r_mcangle_it1.287
r_mcbond_it0.733
r_chiral_restr0.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.432
r_dihedral_angle_4_deg18.718
r_dihedral_angle_3_deg11.076
r_dihedral_angle_1_deg5.577
r_scangle_it3.308
r_scbond_it2.101
r_angle_refined_deg1.4
r_mcangle_it1.287
r_mcbond_it0.733
r_chiral_restr0.096
r_bond_refined_d0.014
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2336
Nucleic Acid Atoms
Solvent Atoms419
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction