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The von Willebrand factor A domain of human capillary morphogenesis gene II, flexibly fused to the 1TEL crystallization chaperone, Thr-Val linker variant, Expressed with SUMO tag
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QAR 1TEL experimental model PDB 1SHT vWa
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 0.1M HEPES 2.0M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.46 49.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.096 α = 90 b = 164.096 β = 90 c = 54.401 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 2022-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 71.06 90.48 0.1787 0.05901 0.998 4.67 10.1 66252 24.16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.968 2.574 2.709 0.607
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.9 71.06 1.33 59958 3116 90.48 0.2392 0.2377 0.2389 0.2664 0.2674 29.15
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 10.6663 f_angle_d 0.6601 f_chiral_restr 0.0427 f_plane_restr 0.0045 f_bond_d 0.0039
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5823 Nucleic Acid Atoms Solvent Atoms 827 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection autoPROC data reduction autoPROC data scaling PHASER phasing Coot model building