5CMX

X-ray structure of the complex between human alpha thrombin and a duplex/quadruplex 31-mer DNA aptamer


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72930.2 M sodium malonate pH 7, 18 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2344.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.319α = 90
b = 124.42β = 90
c = 40.44γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442014-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.987090.10.1347.33.27828
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.983.1185.50.5582.32.9

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 REPLACEMENTTHROUGHOUT4DII2.9865.67740641192.60.1690.1660.231RANDOM54.54
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]
0.84-0.8-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.004
r_dihedral_angle_3_deg18.414
r_dihedral_angle_4_deg18.333
r_dihedral_angle_1_deg7.469
r_long_range_B_refined7.125
r_long_range_B_other7.089
r_scangle_other4.598
r_mcangle_it4.005
r_mcangle_other4.003
r_scbond_it2.838
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.004
r_dihedral_angle_3_deg18.414
r_dihedral_angle_4_deg18.333
r_dihedral_angle_1_deg7.469
r_long_range_B_refined7.125
r_long_range_B_other7.089
r_scangle_other4.598
r_mcangle_it4.005
r_mcangle_other4.003
r_scbond_it2.838
r_scbond_other2.822
r_mcbond_it2.452
r_mcbond_other2.451
r_angle_refined_deg1.719
r_angle_other_deg1.2
r_chiral_restr0.101
r_bond_refined_d0.011
r_bond_other_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2245
Nucleic Acid Atoms612
Solvent Atoms70
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing