6UDB

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 DROP6.5298500 ul of 0.1 M Bis-Tris, pH 6.5, 25% w/v polyethylene glycol 3350 in the reservoir with 2 ul of reservoir buffer mixed with 2 ul of 10 mg/ml of protein in the drop
Crystal Properties
Matthews coefficientSolvent content
1.9737.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.458α = 90
b = 85.555β = 99
c = 58.098γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.000ALS5.0.2

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
11.5542.7899.60.92310.9164849
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)
11.551.580.9381.3

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 REPLACEMENTTHROUGHOUT3RY21.5542.7862823200099.550.1670.16590.2014RANDOM28.433
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]
0.12-0.311.85-1.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.473
r_dihedral_angle_4_deg19.673
r_dihedral_angle_3_deg13.686
r_dihedral_angle_1_deg7.28
r_angle_refined_deg2.147
r_chiral_restr0.172
r_bond_refined_d0.022
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3590
Nucleic Acid Atoms
Solvent Atoms451
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing