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Re-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antagonist Eptifibatide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TXV PDB ENTRY 1TXV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 11% PEG 3350, 0.7 M MAGNESIUM ACETATE, 0.1 M IMIDAZOLE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
Crystal Properties Matthews coefficient Solvent content 3.8 67.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.593 α = 90 b = 149.593 β = 90 c = 175.683 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD MIRROR 2003-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.9 50 100 0.15 14.9 7 50647
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 100 0.62 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1TXV 2.9 47.19 46249 2421 96.1 0.166 0.163 0.1698 0.213 0.2162 RANDOM 44.6
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] 0.89 0.44 0.89 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.968 r_dihedral_angle_4_deg 13.632 r_dihedral_angle_3_deg 11.724 r_dihedral_angle_1_deg 5.174 r_mcangle_it 2.14 r_scangle_it 2.062 r_mcbond_it 1.302 r_scbond_it 1.213 r_angle_refined_deg 0.922 r_angle_other_deg 0.759
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.968 r_dihedral_angle_4_deg 13.632 r_dihedral_angle_3_deg 11.724 r_dihedral_angle_1_deg 5.174 r_mcangle_it 2.14 r_scangle_it 2.062 r_mcbond_it 1.302 r_scbond_it 1.213 r_angle_refined_deg 0.922 r_angle_other_deg 0.759 r_nbd_refined 0.178 r_nbd_other 0.17 r_nbtor_refined 0.17 r_symmetry_vdw_other 0.167 r_symmetry_vdw_refined 0.133 r_xyhbond_nbd_refined 0.128 r_symmetry_hbond_refined 0.128 r_nbtor_other 0.078 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 10342 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 205
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing