5EW1

Human thrombin sandwiched between two DNA aptamers: HD22 and HD1-deltaT3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4I7Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529828% MPEG 2000, 0.1 M Bis/Tris pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.7355.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.548α = 90
b = 145.548β = 90
c = 145.548γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442014-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.95501000.1840.1890.044.621.610960
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.953.061000.7490.7690.170.91920.21078

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 REPLACEMENTTHROUGHOUT4I7Y2.95501031758699.430.15840.15550.208RANDOM50.954
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_deg35.274
r_dihedral_angle_3_deg16.685
r_dihedral_angle_4_deg13.959
r_dihedral_angle_1_deg6.811
r_mcangle_it3.116
r_angle_refined_deg2.006
r_mcbond_it1.959
r_mcbond_other1.958
r_angle_other_deg1.293
r_chiral_restr0.114
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.274
r_dihedral_angle_3_deg16.685
r_dihedral_angle_4_deg13.959
r_dihedral_angle_1_deg6.811
r_mcangle_it3.116
r_angle_refined_deg2.006
r_mcbond_it1.959
r_mcbond_other1.958
r_angle_other_deg1.293
r_chiral_restr0.114
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2243
Nucleic Acid Atoms851
Solvent Atoms74
Heterogen Atoms46

Software

Software
Software NamePurpose
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing