3VXF

X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5


X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5298THE CRYSTAL WAS OBTAINED BY A SITTING DROP VAPOR DIFFUSION AFTER MACROSEEDING. 2% (W/V) TO 10% (W/V) PEG4000, 100MM SODIUM ACETATE PD5.0. THE INITIAL CONCENTRATION OF THROMBIN-BIVALIRUDIN COMPLEX WAS 5MG/ML, pH 5.00, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.998α = 90
b = 107.8β = 90
c = 45.888γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDADSC QUANTUM 4rBending magnet, monochromator, mirrors2009-06-13MSINGLE WAVELENGTH
22neutron298IMAGE PLATEBIX-4monochromator2009-03-23M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A1.0Photon FactoryBL-6A
2NUCLEAR REACTORJRR-3M BEAMLINE 1G-C2.6JRR-3M1G-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)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
11.65095.60.05134.55118251182-3
22.8100800.1344.79850920.03
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.660.3325.2
11.661.720.2436.8
11.721.80.17310.9
11.81.90.12513.8
11.92.020.08817.9
12.022.170.06822.7
12.172.390.05629.1
12.392.740.04739.7
12.743.450.0444.9
13.45500.03645.6
22.82.90.331.81

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 DIFFRACTION1.60229.2271.355113651136190295.320.16190.16090.184217.899
NEUTRON DIFFRACTION2.75244.873807240473.720.18550.18280.233915.603
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]
-1.01672.9256-1.9089
0.7967-2.71111.9144
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.995
f_angle_d2.044
f_chiral_restr0.117
f_bond_d0.016
f_plane_restr0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2357
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms14

Software

Software
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling