6UD1

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 1SWC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3.5298500 ul of 0.1 M Citric Acid, pH 3.5, 3M NaCl in the 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
2.4549.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.351α = 90
b = 57.351β = 90
c = 172.32γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-08-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID1.000APS19-ID

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
11.5586.1699.90.99914.310.3400052
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)
11.551.580.7942.3

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 REPLACEMENTTHROUGHOUT1swc1.5586.1638025196899.830.16740.16620.1918RANDOM25.13
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
r_dihedral_angle_2_deg30.545
r_dihedral_angle_4_deg19.166
r_dihedral_angle_3_deg16.944
r_dihedral_angle_1_deg7.898
r_mcangle_it5.234
r_angle_other_deg4.008
r_mcbond_it3.33
r_mcbond_other3.33
r_angle_refined_deg2.467
r_chiral_restr0.155
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.545
r_dihedral_angle_4_deg19.166
r_dihedral_angle_3_deg16.944
r_dihedral_angle_1_deg7.898
r_mcangle_it5.234
r_angle_other_deg4.008
r_mcbond_it3.33
r_mcbond_other3.33
r_angle_refined_deg2.467
r_chiral_restr0.155
r_bond_refined_d0.027
r_gen_planes_other0.025
r_gen_planes_refined0.014
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1794
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms2

Software

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