2VDN

Re-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antagonist Eptifibatide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TXVPDB ENTRY 1TXV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527711% PEG 3350, 0.7 M MAGNESIUM ACETATE, 0.1 M IMIDAZOLE, 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 = 149.593α = 90
b = 149.593β = 90
c = 175.683γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRROR2003-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A1CHESSA1

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
12.9501000.1514.9750647
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)
12.931000.622.7

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1TXV2.947.1946249242196.10.1660.1630.213RANDOM44.6
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]
0.890.440.89-1.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.968
r_dihedral_angle_4_deg13.632
r_dihedral_angle_3_deg11.724
r_dihedral_angle_1_deg5.174
r_mcangle_it2.14
r_scangle_it2.062
r_mcbond_it1.302
r_scbond_it1.213
r_angle_refined_deg0.922
r_angle_other_deg0.759
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.968
r_dihedral_angle_4_deg13.632
r_dihedral_angle_3_deg11.724
r_dihedral_angle_1_deg5.174
r_mcangle_it2.14
r_scangle_it2.062
r_mcbond_it1.302
r_scbond_it1.213
r_angle_refined_deg0.922
r_angle_other_deg0.759
r_nbd_refined0.178
r_nbd_other0.17
r_nbtor_refined0.17
r_symmetry_vdw_other0.167
r_symmetry_vdw_refined0.133
r_xyhbond_nbd_refined0.128
r_symmetry_hbond_refined0.128
r_nbtor_other0.078
r_chiral_restr0.057
r_bond_refined_d0.005
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 Atoms10342
Nucleic Acid Atoms
Solvent Atoms364
Heterogen Atoms205

Software

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