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Crystal structure of alpha6beta1 integrin headpiece
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WK0 4wk0, 3vi3, 5xcx experimental model PDB 3VI3 4wk0, 3vi3, 5xcx experimental model PDB 5XCX 4wk0, 3vi3, 5xcx
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 23% PEG1000, 0.2 M NaCl, 0.1 M Na/K phosphate, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.93 58.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.52 α = 90 b = 251.31 β = 90 c = 63.25 γ = 90
Symmetry Space Group P 21 21 2
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 RAYONIX MX300-HS 2017-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1.0 NSRRC TPS 05A
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 2.89 47.8 99.6 0.158 0.997 12.48 9.75 42251 72.74
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 2.89 3.07 0.806 1.63
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4wk0, 3vi3, 5xcx 2.89 44.57 1.34 42218 2038 99.54 0.2088 0.2066 0.2069 0.2486 0.2498 78.68
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 11.7692 f_angle_d 0.7737 f_chiral_restr 0.0546 f_plane_restr 0.0048 f_bond_d 0.0039
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9540 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 89
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing