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Structure of the 4-CHRD domain of human Chordin in complex with a Heparin Oligosaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277.15 0.1M Imidazole/MES buffer pH 6.5,
0.06M Magnesium chloride hexahydrate/Calcium chloride dihydrate, 30% Glycerol/PEG 4000.
(Morpheus condition A3). 50ug/mL Heparin Dp4. 2 VAPOR DIFFUSION, SITTING DROP 6.5 277.15 0.1M Imidazole/MES buffer pH 6.5,
0.06M Magnesium chloride hexahydrate/Calcium chloride dihydrate, 30% Glycerol/PEG 4000.
(Morpheus condition A3). 50ug/mL Heparin Dp4.
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.774 α = 90 b = 172.774 β = 90 c = 129.411 γ = 120
Symmetry Space Group P 62 2 2
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 EIGER2 XE 16M 2024-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
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 2.92 97.88 100 0.233 1 17.7 78.9 25297 112.67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.92 3.1 100 0.803 0.53 1 81.3
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 2.92 74.81 1.34 25240 1300 99.9 0.2411 0.2394 0.2406 0.2742 0.2738
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 13.747 f_angle_d 0.789 f_chiral_restr 0.053 f_plane_restr 0.009 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3652 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 116
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building