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Crystal structure of the 4CHRD domain of human chordin, mutant designed to abolish binding to sulphated glycosaminoglycans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Alphafold 3 server prediction of construct
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277.15 0.1M Bis Tris propane pH 8.5, 0.2M Sodium malonate dibasic monohydrate, 20% PEG 3350
PACT condition H12
Crystal Properties Matthews coefficient Solvent content 4.3 71.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.142 α = 90 b = 123.8 β = 90 c = 123.787 γ = 90
Symmetry Space Group I 2 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 99 PIXEL DECTRIS EIGER2 XE 16M 2025-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
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 2.72 61.89 96.7 0.09 0.094 0.035 0.999 13.8 13.5 24327 87
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.72 2.85 89.2 2.195 0.768 1
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 2.72 61.89 1.34 24227 2513 95.89 0.2419 0.2374 0.2306 0.2794 0.2684 127.11
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 13.6826 f_angle_d 0.6164 f_chiral_restr 0.0425 f_plane_restr 0.0052 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3536 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 85
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing