1JMO

Crystal Structure of the Heparin Cofactor II-S195A Thrombin Complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherN-terminal half of native heparin cofactor II and native S195A thrombin

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.4298NH4Cl, PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal Properties
Matthews coefficientSolvent content
4.6873.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 152.31α = 90
b = 152.31β = 90
c = 126.8γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4mirrors2001-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.11.4880SRSPX14.1

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
12.23091.20.0860.0816.56.284555770772151.2
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)
12.212.3562.50.5390.4341.52.216159

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTN-terminal half of native heparin cofactor II and native S195A thrombin2.229.44845557707798391.20.2050.211random55
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]
4.26.153.02-7.22
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it3.794
c_mcangle_it2.452
c_scbond_it2.428
c_mcbond_it1.45
c_angle_deg1.406
c_bond_d0.0063
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5930
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms97

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNSrefinement
CCP4data scaling