2VDP

Integrin AlphaIIbBeta3 Headpiece Bound to Fibrinogen Gamma chain peptide,LGGAKQAGDV


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527711% PEG 3350, 0.7 M MAGNESIUM ACETATE, 0.1 M SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
Crystal Properties
Matthews coefficientSolvent content
3.867.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 148.429α = 90
b = 148.429β = 90
c = 177.16γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCUSTOM (SBC2 3K)MIRROR2004-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-IDAPS19-ID

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
12.85099.40.1116.26.555536
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.899.60.622.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONOTHERTHROUGHOUTNONE2.846.2351563274797.30.1580.1560.204RANDOM48.02
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]
1.320.661.32-1.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.45
r_dihedral_angle_4_deg13.921
r_dihedral_angle_3_deg12.317
r_dihedral_angle_1_deg5.468
r_mcangle_it2.702
r_scangle_it2.486
r_mcbond_it1.677
r_scbond_it1.567
r_angle_refined_deg0.988
r_angle_other_deg0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.45
r_dihedral_angle_4_deg13.921
r_dihedral_angle_3_deg12.317
r_dihedral_angle_1_deg5.468
r_mcangle_it2.702
r_scangle_it2.486
r_mcbond_it1.677
r_scbond_it1.567
r_angle_refined_deg0.988
r_angle_other_deg0.77
r_nbd_refined0.181
r_nbd_other0.174
r_nbtor_refined0.171
r_symmetry_vdw_other0.165
r_xyhbond_nbd_refined0.127
r_symmetry_hbond_refined0.112
r_symmetry_vdw_refined0.104
r_nbtor_other0.08
r_chiral_restr0.061
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10337
Nucleic Acid Atoms
Solvent Atoms557
Heterogen Atoms205

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing