5F2B

Expanding Nature's Catalytic Repertoire -Directed Evolution of an Artificial Metalloenzyme for In Vivo Metathesis


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42931.5 M ammonium sulfate, 0.1 M sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.1643.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.465α = 90
b = 57.465β = 90
c = 173.564γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2015-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.000SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.754.5531000.1030.030.99812.612.616547
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.731002.0180.5770.5091.313837

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 REPLACEMENTTHROUGHOUT2QCB1.754.551576476099.970.14650.14370.2058RANDOM37.888
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]
-2.32-2.324.64
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free65.16
r_dihedral_angle_2_deg26.327
r_sphericity_bonded25.539
r_dihedral_angle_3_deg13.999
r_dihedral_angle_4_deg12.942
r_mcangle_it8.362
r_dihedral_angle_1_deg7.458
r_mcbond_it7.06
r_mcbond_other6.963
r_rigid_bond_restr6.452
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free65.16
r_dihedral_angle_2_deg26.327
r_sphericity_bonded25.539
r_dihedral_angle_3_deg13.999
r_dihedral_angle_4_deg12.942
r_mcangle_it8.362
r_dihedral_angle_1_deg7.458
r_mcbond_it7.06
r_mcbond_other6.963
r_rigid_bond_restr6.452
r_angle_refined_deg2.62
r_angle_other_deg1.322
r_chiral_restr0.171
r_bond_refined_d0.032
r_gen_planes_refined0.011
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms915
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms53

Software

Software
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction