4OW3

Thermolysin structure determined by free-electron laser


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2TLI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION6.5298300 ul of the protein stock was mixed in a 1:1 ratio with 40% PEG 2000, 100 mM MES pH 6.5, 5 mM CaCl2. Crystallization occurred within minutes.
Crystal Properties
Matthews coefficientSolvent content
2.3848.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.8933α = 90
b = 92.8933β = 90
c = 130.438γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELCS-PAD detector2011-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE CXI1.269, 1.297SLAC LCLSCXI

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.168.599.150.22091986114.3263474589
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1891.25.64.5

Refinement

Statistics
Diffraction IDStructure Solution 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 REPLACEMENT2TLI2.168.47233334231.4417309784319861104299.03266018450.2196541618840.2172426708150.26316848463316.2875323051
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_d12.8953940052
f_angle_d0.682438849813
f_chiral_restr0.025759577597
f_bond_d0.00289852909819
f_plane_restr0.00240657682604
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2404
Nucleic Acid Atoms
Solvent Atoms338
Heterogen Atoms5

Software

Software
Software NamePurpose
PHENIXrefinement