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Crystal structure of an engineered VWF A2 domain (N1493C and C1670S)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AO3 PDB ENTRY 1AO3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 293 0.1M sodium citrate, 1.6M (NH4)2SO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.34 47.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.759 α = 90 b = 69.759 β = 90 c = 73.605 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 RAYONIX MX225HE 2009-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 1.0000 SSRF BL17U
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 1.9 50 97 0.103 20.9 8.5 15647
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 1.9 1.97 87.5 0.469 2.5 4.9
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 PDB ENTRY 1AO3 1.9 46.7 15645 781 97.19 0.203 0.2015 0.2022 0.2313 0.2004 RANDOM 22.9745
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] 0.56 0.28 0.56 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.785 r_dihedral_angle_3_deg 13.916 r_dihedral_angle_4_deg 8.603 r_dihedral_angle_1_deg 5.529 r_scangle_it 4.952 r_scbond_it 3.251 r_rigid_bond_restr 2.738 r_mcangle_it 2.507 r_mcbond_it 1.424 r_angle_refined_deg 1.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.785 r_dihedral_angle_3_deg 13.916 r_dihedral_angle_4_deg 8.603 r_dihedral_angle_1_deg 5.529 r_scangle_it 4.952 r_scbond_it 3.251 r_rigid_bond_restr 2.738 r_mcangle_it 2.507 r_mcbond_it 1.424 r_angle_refined_deg 1.111 r_sphericity_bonded 0.676 r_sphericity_free 0.558 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.207 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.138 r_xyhbond_nbd_refined 0.125 r_metal_ion_refined 0.106 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1441 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing