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Crystal structure of integrin avb6 headpiece in complex with compound 12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UM9 experimental model PDB 4O02
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 13% PEG 3350, 100 mM HEPES pH 7.1, 200 mM ammonium citrate
Crystal Properties Matthews coefficient Solvent content 3.3 62.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.494 α = 90 b = 132.501 β = 90 c = 168.366 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 9M 2022-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.920105 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.57 52.06 99.88 0.996 8.36 7.5 69516 62.27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.57 2.662 0.369
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.57 52.06 1.34 69369 3422 99.81 0.217 0.2161 0.2342 0.2229
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 18.569 f_angle_d 0.65 f_chiral_restr 0.047 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11434 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 332
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing