6U18

Directed evolution of a biosensor selective for the macrolide antibiotic clarithromycin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3G56PDB entry 3G56

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529310% PEG3350, 0.1 M ammonium citrate dibasic
Crystal Properties
Matthews coefficientSolvent content
2.1442.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.897α = 90
b = 53.161β = 90
c = 158.815γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS EIGER R 4MRigaku Varimax-HF Arc2019-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5419

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
1229.1499.90.0480.0520.0210.99922.86.12543423.91
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0599.90.2920.3210.1320.9595.35.7

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-VALUEPDB entry 3G56229.141.3425374130899.890.20290.20190.220733.72
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_d12.9086
f_angle_d0.6143
f_chiral_restr0.0374
f_bond_d0.004
f_plane_restr0.0032
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2806
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms117

Software

Software
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
CrysalisProdata collection
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing