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Crystal structure of the von Willebrand factor A3 domain in complex with a collagen III derived triple-helical peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ATZ 1ATZ & 4DMT experimental model PDB 4DMT 1ATZ & 4DMT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 100 mM cacodylate, pH 6.5, 1.20 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.69 54.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.614 α = 90 b = 187.614 β = 90 c = 89.373 γ = 120
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 2006-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9395 ESRF ID14-4
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 2.8 46.9 92.5 0.081 14.9 7 41019 41019 3 67.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 73.1 0.452 2.3 3 4679
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1ATZ & 4DMT 2.8 46.32 38880 38880 2090 92.23 0.20416 0.20154 0.1986 0.2531 0.2524 RANDOM - not-related by twinning 46.995
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] -19.75 -19.75 39.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.892 r_dihedral_angle_3_deg 18.633 r_dihedral_angle_4_deg 18.266 r_dihedral_angle_1_deg 6.512 r_angle_refined_deg 1.649 r_scangle_it 1.379 r_angle_other_deg 0.922 r_scbond_it 0.897 r_mcangle_it 0.433 r_mcbond_it 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.892 r_dihedral_angle_3_deg 18.633 r_dihedral_angle_4_deg 18.266 r_dihedral_angle_1_deg 6.512 r_angle_refined_deg 1.649 r_scangle_it 1.379 r_angle_other_deg 0.922 r_scbond_it 0.897 r_mcangle_it 0.433 r_mcbond_it 0.26 r_mcbond_other 0.1 r_chiral_restr 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11631 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 20
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling