3IJE

Crystal structure of the complete integrin alhaVbeta3 ectodomain plus an Alpha/beta transmembrane fragment


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JV2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.829812% PEG3350, 0.1M Na acetate, 0.8M NaCl, 2.5mM CaCl2, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
4.0569.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.87α = 90
b = 129.87β = 90
c = 305.9γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID1.0332APS19-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
12.950930.0888.956670211

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 REPLACEMENTTHROUGHOUT1JV22.920590835908329171000.246370.244470.28482RANDOM45.773
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]
-1.45-0.73-1.452.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.54
r_dihedral_angle_3_deg17.241
r_dihedral_angle_4_deg11.941
r_dihedral_angle_1_deg6.415
r_scangle_it1.476
r_angle_refined_deg1.13
r_angle_other_deg0.808
r_scbond_it0.74
r_mcangle_it0.455
r_mcbond_it0.243
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.54
r_dihedral_angle_3_deg17.241
r_dihedral_angle_4_deg11.941
r_dihedral_angle_1_deg6.415
r_scangle_it1.476
r_angle_refined_deg1.13
r_angle_other_deg0.808
r_scbond_it0.74
r_mcangle_it0.455
r_mcbond_it0.243
r_nbd_refined0.198
r_nbd_other0.176
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.148
r_symmetry_vdw_other0.147
r_metal_ion_refined0.13
r_symmetry_vdw_refined0.123
r_symmetry_hbond_refined0.099
r_nbtor_other0.092
r_chiral_restr0.065
r_mcbond_other0.028
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_xyhbond_nbd_other0.002
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12632
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms455

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing