3P6Z

Structural basis of thrombin mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293100 mM MOPS/HEPES-Na, pH 7.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) 2-methylpentane-2,4-diol (MPD), 30 mM Ca2+, 30 mM Mg2+, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3948.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.208α = 99.38
b = 62.259β = 110.46
c = 67.51γ = 92.26
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDADSC QUANTUM 315r2009-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9725ESRFID23-1

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
11.6962.1494.20.0812.33.38682481788
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.6961.7989.6

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-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1PPB1.731.928178879739204794.490.200590.200590.19960.23876RANDOM27.861
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.072
r_dihedral_angle_3_deg16.216
r_dihedral_angle_4_deg15.686
r_dihedral_angle_1_deg7.349
r_scangle_it4.81
r_scbond_it3.166
r_mcangle_it2.075
r_angle_refined_deg2.032
r_mcbond_it1.3
r_chiral_restr0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.072
r_dihedral_angle_3_deg16.216
r_dihedral_angle_4_deg15.686
r_dihedral_angle_1_deg7.349
r_scangle_it4.81
r_scbond_it3.166
r_mcangle_it2.075
r_angle_refined_deg2.032
r_mcbond_it1.3
r_chiral_restr0.15
r_bond_refined_d0.023
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4733
Nucleic Acid Atoms
Solvent Atoms505
Heterogen Atoms108

Software

Software
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling