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Re-refinement of Integrin AlphaIIbBeta3 Headpiece
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 SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
Crystal Properties Matthews coefficient Solvent content 3.7 66.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.869 α = 90 b = 148.869 β = 90 c = 176.137 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 2003-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 2.8 50 99.9 0.13 14 7.5 55875
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 2.8 2.9 99.9 0.68 3.1
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 2.8 42.64 50725 2713 95.5 0.164 0.161 0.1666 0.205 0.2061 RANDOM 17.09
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 0.61 1.21 -1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.211 r_dihedral_angle_4_deg 13.472 r_dihedral_angle_3_deg 11.618 r_dihedral_angle_1_deg 5.264 r_mcangle_it 2.222 r_scangle_it 2.093 r_mcbond_it 1.391 r_scbond_it 1.293 r_angle_refined_deg 0.936 r_angle_other_deg 0.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.211 r_dihedral_angle_4_deg 13.472 r_dihedral_angle_3_deg 11.618 r_dihedral_angle_1_deg 5.264 r_mcangle_it 2.222 r_scangle_it 2.093 r_mcbond_it 1.391 r_scbond_it 1.293 r_angle_refined_deg 0.936 r_angle_other_deg 0.758 r_nbd_refined 0.179 r_nbd_other 0.171 r_nbtor_refined 0.171 r_symmetry_vdw_other 0.152 r_symmetry_hbond_refined 0.135 r_xyhbond_nbd_refined 0.124 r_symmetry_vdw_refined 0.112 r_nbtor_other 0.078 r_chiral_restr 0.058 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 10285 Nucleic Acid Atoms Solvent Atoms 612 Heterogen Atoms 210
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing