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High-resolution crystal structure of fluoropropylated cystine knot, binding to alpha-5 beta-6 integrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2N8C PDB entries 2N8C & 2N8B experimental model PDB 2N8B PDB entries 2N8C & 2N8B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 298 Isopropanol
Crystal Properties Matthews coefficient Solvent content 1.59 22.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 16.95 α = 90 b = 44.25 β = 90 c = 66.41 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 298 CMOS RDI CMOS_8M 2016-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.000 ALS 4.2.2
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 1 36.82 94.1 0.036 32.3 29 27921
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 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 entries 2N8C & 2N8B 1 36.82 25665 1341 96.72 0.204 0.2029 0.203 0.2257 0.2226 RANDOM 10.152
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 24.686 r_dihedral_angle_2_deg 18.835 r_dihedral_angle_3_deg 11.798 r_dihedral_angle_1_deg 11.462 r_angle_refined_deg 3.366 r_angle_other_deg 1.703 r_chiral_restr 0.531 r_bond_refined_d 0.032 r_gen_planes_refined 0.016 r_bond_other_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 24.686 r_dihedral_angle_2_deg 18.835 r_dihedral_angle_3_deg 11.798 r_dihedral_angle_1_deg 11.462 r_angle_refined_deg 3.366 r_angle_other_deg 1.703 r_chiral_restr 0.531 r_bond_refined_d 0.032 r_gen_planes_refined 0.016 r_bond_other_d 0.008 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 529 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing