6THS

High resolution crystal structure of Leaf-branch cutinase S165A variant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4EB0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION92850.1 M Bicine pH 9.0, 2% Dioxane, 12% PEG 20000
Crystal Properties
Matthews coefficientSolvent content
2.244.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.604α = 90
b = 109.604β = 90
c = 35.287γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-06-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97907ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.147.5199.60.0670.070.99918.0612.7119870015.012
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.11.1697.50.5850.6110.9143.2711.913

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 REPLACEMENTTHROUGHOUT4EB01.147.5183724439788.960.13770.13620.1671RANDOM15.091
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]
0.940.470.94-3.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.867
r_sphericity_free24.204
r_sphericity_bonded16.923
r_dihedral_angle_4_deg13.989
r_dihedral_angle_3_deg9.99
r_dihedral_angle_1_deg6.594
r_rigid_bond_restr4.644
r_angle_refined_deg1.764
r_angle_other_deg1.162
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.867
r_sphericity_free24.204
r_sphericity_bonded16.923
r_dihedral_angle_4_deg13.989
r_dihedral_angle_3_deg9.99
r_dihedral_angle_1_deg6.594
r_rigid_bond_restr4.644
r_angle_refined_deg1.764
r_angle_other_deg1.162
r_chiral_restr0.107
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1961
Nucleic Acid Atoms
Solvent Atoms290
Heterogen Atoms6

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction