6TEJ

Structure of apo IrtAB devoid SID in complex with sybody Syb_NL5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4Q4H 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
3VAPOR DIFFUSION, SITTING DROP7.527728% (V/V) PEG 400, 0.2M NaCl, 0.1M HEPES
Crystal Properties
Matthews coefficientSolvent content
1.9235.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.06α = 90
b = 78.58β = 98.2
c = 133.57γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
13x-ray100PIXELDECTRIS PILATUS 2M-F2018-09-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.000SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
12.747.4399.90.1050.1140.99915.036.8475837672.353
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.771001.6881.8250.681.216.928

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 REPLACEMENTTHROUGHOUT4q4h2.747.431.3658326291699.870.26550.26380.296192.1334
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9334
Nucleic Acid Atoms
Solvent Atoms54
Heterogen Atoms34

Software

Software
Software NamePurpose
PHENIXrefinement
Cootmodel building
XSCALEdata reduction
XSCALEdata scaling
PHASERphasing
XDSdata collection