☰ Navigation Tabs
Crystal structure of Glycoprotein VI in complex with collagen-peptide (GPO)5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.1 M MES pH 6.0
0.2 M MgCl2
20% (w/v) PEG-6000
Crystal Properties Matthews coefficient Solvent content 3.35 63.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.97 α = 90 b = 59.97 β = 90 c = 313.212 γ = 90
Symmetry Space Group P 41 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 ADSC QUANTUM 315r 2013-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 ESRF ID23-1
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 2.5 78.3 99.5 0.121 0.995 9.7 7.9 20736 34.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.61 99.8 1.03 0.535 1.8 7.4
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 5OU7 2.5 78.3 19700 1022 99.03 0.21051 0.20814 0.2128 0.25739 0.2535 RANDOM 58.428
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] -0.28 -0.28 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.965 r_dihedral_angle_4_deg 22.325 r_dihedral_angle_3_deg 15.304 r_dihedral_angle_1_deg 6.894 r_long_range_B_refined 5.668 r_long_range_B_other 5.636 r_mcangle_it 3.399 r_mcangle_other 3.399 r_scangle_other 3.31 r_scbond_it 2.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.965 r_dihedral_angle_4_deg 22.325 r_dihedral_angle_3_deg 15.304 r_dihedral_angle_1_deg 6.894 r_long_range_B_refined 5.668 r_long_range_B_other 5.636 r_mcangle_it 3.399 r_mcangle_other 3.399 r_scangle_other 3.31 r_scbond_it 2.026 r_scbond_other 2.025 r_mcbond_it 2.009 r_mcbond_other 2.008 r_angle_refined_deg 1.635 r_angle_other_deg 1.093 r_chiral_restr 0.121 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2959 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing