3H32

Crystal structure of D-dimer from human fibrin complexed with Gly-His-Arg-Pro-Tyr-amide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FZEPDB entry 1FZE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5295Equal volumes of (a) 5 mg/mL D-dimer, 0.5 mM GHRPYam, 0.3 mM GPRPam, 0.05 M Tris-HCl pH 8.0 and (b) 1% PEG 3350, 1 mM Iodoacetamide, 1 mM CaCl2, 2mM Sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.2261.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 264.72α = 90
b = 97.32β = 122.78
c = 132.49γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.31.0000ALS5.0.3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.650950.0733.6331003158411

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1FZE3.6503158425002124475.50.26310.26310.3199random
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
c_angle_deg1.679
c_bond_d0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11030
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms216

Software

Software
Software NamePurpose
ADSCdata collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling