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Crystal structure of the orphan region of human endoglin/CD105
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SEX 3SEX, 3SET, 4WRN experimental model PDB 3SET 3SEX, 3SET, 4WRN experimental model PDB 4WRN 3SEX, 3SET, 4WRN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 30% PEG 1000, 0.1 M TRIS-HCL
Crystal Properties Matthews coefficient Solvent content 3.02 57.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.15 α = 90 b = 114.15 β = 90 c = 120.62 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 2014-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.42 45.74 99.1 0.046 11.76 3.4 33737 -3 70.03
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 2.42 2.49 98.5 0.811 1.25 3.5
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3SEX, 3SET, 4WRN 2.42 45.737 1.39 33699 1636 99.05 0.2223 0.2202 0.2244 0.2627 0.2616 Random selection 76.6
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 10.818 f_angle_d 0.554 f_chiral_restr 0.042 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5117 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 67
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing