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Crystal structure of a VWF binding collagen III derived triple helical peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V7H 1V7H poly-ala
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.95-1.0 M ammonium tartrate , VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.71 27.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.33 α = 90 b = 24.43 β = 103.11 c = 39.32 γ = 90
Symmetry Space Group P 1 21 1
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 2008-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.975 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 1.39 38.29 99.8 0.107 13.8 6.9 11914 11914 -3.7 8.3
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 1.39 1.47 99.6 0.572 3.8 6.3 1721
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 1V7H poly-ala 1.39 38.29 11334 11334 570 99.78 0.10847 0.10671 0.1085 0.14466 0.146 RANDOM 7.71
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] -0.32 -0.33 -0.07 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.092 r_dihedral_angle_3_deg 10.104 r_dihedral_angle_4_deg 10.093 r_dihedral_angle_1_deg 4.922 r_scangle_it 3.245 r_scbond_it 2.13 r_angle_refined_deg 1.94 r_mcangle_it 1.382 r_angle_other_deg 1.002 r_mcbond_it 0.921
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.092 r_dihedral_angle_3_deg 10.104 r_dihedral_angle_4_deg 10.093 r_dihedral_angle_1_deg 4.922 r_scangle_it 3.245 r_scbond_it 2.13 r_angle_refined_deg 1.94 r_mcangle_it 1.382 r_angle_other_deg 1.002 r_mcbond_it 0.921 r_rigid_bond_restr 0.807 r_mcbond_other 0.284 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 606 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 24
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling