2H9T

Crystal structure of human alpha-thrombin in complex with suramin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5291100 mM tris, 25 % tert-butanol, 0.16 mM thrombin:suramin complex, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.7855.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.966α = 90
b = 76.202β = 90
c = 113.848γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-10-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX11.438LNLSD03B-MX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.441.031000.180.184.14.91562527.82
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.42.531000.5490.5493.14.92233

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1PPB2.441.033.1149781557978199.980.1840.1840.180.266RANDOM28.664
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.293
r_dihedral_angle_3_deg20.01
r_dihedral_angle_4_deg19.907
r_dihedral_angle_1_deg7.76
r_scangle_it3.524
r_scbond_it2.318
r_angle_refined_deg2.059
r_mcangle_it1.407
r_mcbond_it0.812
r_nbtor_refined0.326
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.293
r_dihedral_angle_3_deg20.01
r_dihedral_angle_4_deg19.907
r_dihedral_angle_1_deg7.76
r_scangle_it3.524
r_scbond_it2.318
r_angle_refined_deg2.059
r_mcangle_it1.407
r_mcbond_it0.812
r_nbtor_refined0.326
r_nbd_refined0.269
r_symmetry_hbond_refined0.265
r_symmetry_vdw_refined0.222
r_xyhbond_nbd_refined0.174
r_chiral_restr0.14
r_bond_refined_d0.019
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2282
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms86

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction