6Z8X

X-ray structure of the complex between human alpha thrombin and a thrombin binding aptamer variant (TBA-3Leu), which contains leucyl amide in the side chain of Thy3 at N3.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PPB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629318% v/v 2-propanol, 18% w/v PEG 4000, 100 mM tri-sodium citrate, pH 5.6
Crystal Properties
Matthews coefficientSolvent content
3.8868.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.671α = 90
b = 94.671β = 90
c = 124.693γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2019-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
12.5381.9991.5110.719.26793
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)
12.532.9677.80.71.818.1

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 REPLACEMENTTHROUGHOUT1PPB2.5381.99612363230.650.2490.24480.2915RANDOM69.54
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]
-0.11-0.05-0.110.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.677
r_dihedral_angle_3_deg18.364
r_dihedral_angle_4_deg13.401
r_dihedral_angle_1_deg6.218
r_angle_refined_deg0.764
r_chiral_restr0.063
r_bond_refined_d0.002
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2176
Nucleic Acid Atoms300
Solvent Atoms3
Heterogen Atoms32

Software

Software
Software NamePurpose
autoPROCdata processing
STARANISOdata processing
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction