2VDM

Re-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antagonist Tirofiban


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527710-12% PEG3350, 0.7 M MAGNESIUM ACETATE, 0.1 M IMIDAZOLE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
Crystal Properties
Matthews coefficientSolvent content
3.867.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 148.577α = 90
b = 148.577β = 90
c = 177.239γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCUSTOM (SBC2 3K)MIRROR2003-10-04MSINGLE 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
12.95099.80.1412.1750516
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)
12.9398.20.5826

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 1TXV2.946.23467762464970.1690.1670.206RANDOM42.7
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]
1.210.61.21-1.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.665
r_dihedral_angle_4_deg13.904
r_dihedral_angle_3_deg11.839
r_dihedral_angle_1_deg5.267
r_mcangle_it2.056
r_scangle_it1.907
r_mcbond_it1.244
r_scbond_it1.154
r_angle_refined_deg0.925
r_angle_other_deg0.759
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.665
r_dihedral_angle_4_deg13.904
r_dihedral_angle_3_deg11.839
r_dihedral_angle_1_deg5.267
r_mcangle_it2.056
r_scangle_it1.907
r_mcbond_it1.244
r_scbond_it1.154
r_angle_refined_deg0.925
r_angle_other_deg0.759
r_nbd_refined0.18
r_nbtor_refined0.17
r_nbd_other0.169
r_symmetry_vdw_other0.148
r_xyhbond_nbd_refined0.122
r_symmetry_hbond_refined0.113
r_symmetry_vdw_refined0.099
r_nbtor_other0.08
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 Atoms10291
Nucleic Acid Atoms
Solvent Atoms355
Heterogen Atoms235

Software

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