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Crystal structure of the orphan region of human endoglin/CD105 in complex with BMP9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SEX 3SEX, 5I04, 5I05 experimental model PDB 5I04 3SEX, 5I04, 5I05 experimental model PDB 5I05 3SEX, 5I04, 5I05
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.1 M AMMONIUM TARTRATE
Crystal Properties Matthews coefficient Solvent content 4.14 70.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 211.245 α = 90 b = 211.245 β = 90 c = 53.164 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 PSI PILATUS 6M 2014-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97938 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 4.301 52.811 100 0.395 0.997 3.5 9.5 9558 219
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4.301 4.81 100 0.259 0.6 9.7
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, 5I04, 5I05 4.451 52.811 1.33 8611 847 99.73 0.2888 0.2855 0.2948 0.3181 0.3302 Random selection
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 9.325 f_angle_d 0.634 f_chiral_restr 0.044 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5934 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 51
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing