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Re-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antagonist Tirofiban
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 10-12% PEG3350, 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 67.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.577 α = 90 b = 148.577 β = 90 c = 177.239 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 CUSTOM (SBC2 3K) 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 99.8 0.14 12.1 7 50516
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 98.2 0.58 2 6
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 46.23 46776 2464 97 0.169 0.167 0.1741 0.206 0.204 RANDOM 42.7
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] 1.21 0.6 1.21 -1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.665 r_dihedral_angle_4_deg 13.904 r_dihedral_angle_3_deg 11.839 r_dihedral_angle_1_deg 5.267 r_mcangle_it 2.056 r_scangle_it 1.907 r_mcbond_it 1.244 r_scbond_it 1.154 r_angle_refined_deg 0.925 r_angle_other_deg 0.759
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.665 r_dihedral_angle_4_deg 13.904 r_dihedral_angle_3_deg 11.839 r_dihedral_angle_1_deg 5.267 r_mcangle_it 2.056 r_scangle_it 1.907 r_mcbond_it 1.244 r_scbond_it 1.154 r_angle_refined_deg 0.925 r_angle_other_deg 0.759 r_nbd_refined 0.18 r_nbtor_refined 0.17 r_nbd_other 0.169 r_symmetry_vdw_other 0.148 r_xyhbond_nbd_refined 0.122 r_symmetry_hbond_refined 0.113 r_symmetry_vdw_refined 0.099 r_nbtor_other 0.08 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 10291 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 235
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing