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Crystal structure of human platelet glycoprotein VI in complex with an inhibitory nanobody.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GI7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 283.15 0.2 M calcium acetate, 0.1M sodium cacodylate pH 6.5, 18% PEG8K
Crystal Properties Matthews coefficient Solvent content 2.59 52.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.906 α = 90 b = 84.751 β = 90 c = 124.041 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 283.15 PIXEL DECTRIS PILATUS3 6M 2019-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96864 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.498 84.75 98.6 0.122 0.991 8.67 6.3 26173
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 2.5 2.56 0.834
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2gi7 2.5 70.08 26173 1329 99.893 0.177 0.1742 0.1743 0.2351 0.2349 40.536
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] 0.818 -0.839 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.892 r_dihedral_angle_4_deg 18.373 r_dihedral_angle_3_deg 16.113 r_dihedral_angle_1_deg 8.728 r_lrange_other 8.546 r_lrange_it 8.543 r_scangle_it 5.954 r_scangle_other 5.953 r_mcangle_it 5.236 r_mcangle_other 5.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.892 r_dihedral_angle_4_deg 18.373 r_dihedral_angle_3_deg 16.113 r_dihedral_angle_1_deg 8.728 r_lrange_other 8.546 r_lrange_it 8.543 r_scangle_it 5.954 r_scangle_other 5.953 r_mcangle_it 5.236 r_mcangle_other 5.235 r_scbond_it 3.784 r_scbond_other 3.783 r_mcbond_other 3.369 r_mcbond_it 3.368 r_angle_refined_deg 1.551 r_angle_other_deg 1.211 r_metal_ion_refined 0.197 r_symmetry_nbd_other 0.191 r_nbd_refined 0.186 r_symmetry_nbd_refined 0.181 r_nbd_other 0.172 r_xyhbond_nbd_refined 0.169 r_nbtor_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.114 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.065 r_symmetry_metal_ion_refined 0.028 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4664 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement xia2 data reduction BUCCANEER model building PHASER phasing xia2 data scaling