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Crystal structure of alpha-V beta-1 integrin headpiece in complex with TR01225179
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 28% pentaerythritol ethoxylate (15/4_EO/OH), 0.05M ammonium sulfate, 0.05M Bis Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.27 62.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 199.184 α = 90 b = 148.212 β = 103.18 c = 53.415 γ = 90
Symmetry Space Group C 1 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 PIXEL DECTRIS PILATUS 6M 2019-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.0 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) 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 2.45 48.48 92.3 0.069 0.99 10.1 3.8 51039
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.53 91.1 2.389 0.453 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.45 47.875 1.34 50799 2581 91.75 0.256 0.2549 0.2562 0.2751 0.2771
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.505 f_angle_d 0.755 f_chiral_restr 0.049 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7318 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 209
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PHASER phasing