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Crystal Structure of High-Affinity von Willebrand Factor A1 domain with R1306Q and I1309V Mutations in Complex with High Affinity GPIb alpha
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SQ0 PDB ENTRY 1SQ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 CRYSTALS OF A1/VWD2-GPIBALPA/VWD2 COMPLEX APPEARED IN 12% PEG 8000, 0.1 M SODIUM CACODYLATE PH 6.5, 0.1 M CALCIUM ACETATE, AND 0.4 MG/ML RISTOCETIN (SIGMA-ALDRICH). THESE CRYSTALS WERE CRUSHED AND USED FOR SEEDING. CRYSTALS GREW IN 10 MG/ML COMPLEX, 14% PEG8000, 0.2 M CALCIUM ACETATE, 0.1 M SODIUM CACODYLATE, PH 6.5, AND 0.4 MG/ML RISTOCETIN. NEXT WE SOAKED THESE CRYSTALS IN 14% PEG8000, 0.2 M CALCIUM ACETATE, 0.1 SODIUM CACODYLATE, PH 6.5, AND 4 MG/ML RISTOCETIN.
Crystal Properties Matthews coefficient Solvent content 2.43 49.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.06 α = 90 b = 89.06 β = 90 c = 124.52 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 93 CCD MARRESEARCH 2012-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-BM-B APS 23-BM-B
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 2.08 48.4 99.9 0.09 8.9 2.5 66245 -3 36.97
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 2.08 2.19 99.5 0.74 1.7
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1SQ0 2.081 48.446 1.36 66191 3361 99.88 0.162 0.1605 0.1771 0.189 0.1963
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.977 f_angle_d 0.688 f_chiral_restr 0.026 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3708 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 17
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALEPACK data scaling