6UC3

Spectroscopic and structural characterization of a genetically encoded direct sensor for protein-ligand interactions


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RY2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3.5298500 ul of 0.1 M Citric Acid, pH 3.5, 3M NaCl in reservoir with 2 ul of reservoir buffer mixed with 2 ul of 10 mg/ml of protein in the drop. Crystals were soaked to pH 5.5 overnight with 3 exchanges
Crystal Properties
Matthews coefficientSolvent content
2.1643.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.209α = 90
b = 93.11β = 90
c = 104.369γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6MSi(111) and Si(220) double crystal2019-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.9795SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.8469.4899.20.99816.77.119561
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.849.030.951

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 REPLACEMENTTHROUGHOUT3RY21.8469.481858996998.40.17590.17390.2127RANDOM20.68
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]
0.061.88-1.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.226
r_dihedral_angle_4_deg20.062
r_dihedral_angle_3_deg13.325
r_dihedral_angle_1_deg7.905
r_angle_other_deg4.015
r_mcangle_it3.264
r_mcbond_it2.223
r_mcbond_other2.219
r_angle_refined_deg2.051
r_chiral_restr0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.226
r_dihedral_angle_4_deg20.062
r_dihedral_angle_3_deg13.325
r_dihedral_angle_1_deg7.905
r_angle_other_deg4.015
r_mcangle_it3.264
r_mcbond_it2.223
r_mcbond_other2.219
r_angle_refined_deg2.051
r_chiral_restr0.12
r_bond_refined_d0.02
r_gen_planes_other0.018
r_gen_planes_refined0.01
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1837
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
pointlessdata scaling
PHASERphasing