2VC2

Re-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antagonist L-739758


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% 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
3.968

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 149.151α = 90
b = 149.151β = 90
c = 176.217γ = 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
13.15099.90.1412.1741563
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)
13.13.299.70.562.76

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 1TXV3.142.7238636204497.70.1790.1770.217RANDOM3.21
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]
1.040.521.04-1.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.205
r_dihedral_angle_4_deg14.475
r_dihedral_angle_3_deg13.057
r_dihedral_angle_1_deg5.376
r_scangle_it1.692
r_mcangle_it1.274
r_angle_refined_deg1.001
r_scbond_it0.955
r_mcbond_it0.826
r_angle_other_deg0.765
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.205
r_dihedral_angle_4_deg14.475
r_dihedral_angle_3_deg13.057
r_dihedral_angle_1_deg5.376
r_scangle_it1.692
r_mcangle_it1.274
r_angle_refined_deg1.001
r_scbond_it0.955
r_mcbond_it0.826
r_angle_other_deg0.765
r_nbd_refined0.184
r_nbd_other0.173
r_nbtor_refined0.173
r_symmetry_vdw_other0.147
r_xyhbond_nbd_refined0.136
r_metal_ion_refined0.113
r_symmetry_hbond_refined0.11
r_symmetry_vdw_refined0.103
r_mcbond_other0.1
r_nbtor_other0.081
r_chiral_restr0.058
r_bond_refined_d0.006
r_xyhbond_nbd_other0.005
r_gen_planes_refined0.002
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_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 Atoms10297
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms240

Software

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