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The von Willebrand factor A domain of human capillary morphogenesis gene II, flexibly fused to the 1TEL crystallization chaperone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QB1 2QB1, 1SHU experimental model PDB 1SHU 2QB1, 1SHU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.7 298 100 mM BisTris, 3.0 M NaCl
Crystal Properties Matthews coefficient Solvent content 3.04 59.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.396 α = 90 b = 103.396 β = 90 c = 56.55 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 PIXEL DECTRIS PILATUS 6M 2020-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979460 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.77 38.16 97.1 0.05193 0.05753 0.024 0.999 18.35 5.5 8679 2 71.13
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.77 2.869 97.99 0.6253 0.6876 0.2779 0.899 2.88 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 FREE R-VALUE 2QB1, 1SHU 2.77 38.16 1.34 8679 434 97.16 0.2045 0.2033 0.2005 0.2284 0.2323 75.23
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 12.9234 f_angle_d 0.8562 f_chiral_restr 0.0484 f_bond_d 0.0085 f_plane_restr 0.0066
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1921 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 3
Software Software Software Name Purpose PHENIX refinement Coot model building autoPROC data reduction autoPROC data scaling PHASER phasing