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Re-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antagonist L-739758
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% 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 3.9 68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.151 α = 90 b = 149.151 β = 90 c = 176.217 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 3.1 50 99.9 0.14 12.1 7 41563
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 3.1 3.2 99.7 0.56 2.7 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 3.1 42.72 38636 2044 97.7 0.179 0.177 0.1898 0.217 0.2247 RANDOM 3.21
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] 1.04 0.52 1.04 -1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.205 r_dihedral_angle_4_deg 14.475 r_dihedral_angle_3_deg 13.057 r_dihedral_angle_1_deg 5.376 r_scangle_it 1.692 r_mcangle_it 1.274 r_angle_refined_deg 1.001 r_scbond_it 0.955 r_mcbond_it 0.826 r_angle_other_deg 0.765
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.205 r_dihedral_angle_4_deg 14.475 r_dihedral_angle_3_deg 13.057 r_dihedral_angle_1_deg 5.376 r_scangle_it 1.692 r_mcangle_it 1.274 r_angle_refined_deg 1.001 r_scbond_it 0.955 r_mcbond_it 0.826 r_angle_other_deg 0.765 r_nbd_refined 0.184 r_nbd_other 0.173 r_nbtor_refined 0.173 r_symmetry_vdw_other 0.147 r_xyhbond_nbd_refined 0.136 r_metal_ion_refined 0.113 r_symmetry_hbond_refined 0.11 r_symmetry_vdw_refined 0.103 r_mcbond_other 0.1 r_nbtor_other 0.081 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_xyhbond_nbd_other 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 10297 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 240
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing