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Crystal structure of the 4CHRD domain of human chordin with Anderson-Evans polyoxotungstate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold MR-SAD using AF3 and the W anomalous signal
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277.15 0.1M Morpheus buffer system 3 (Tris/Bicine) pH 8.0, 0.1M Morpheus amino acids (DL-Glutamic acid monohydrate, DL-Alanine, Glycine, DL-Serine and DL-Lysine monohydrochloride). Morpheus condition H11 with 1mM TEW and 0.05 mg/mL Trypsin 2 VAPOR DIFFUSION, SITTING DROP 8.5 277.15 0.1M Morpheus buffer system 3 (Tris/Bicine) pH 8.0, 0.1M Morpheus amino acids (DL-Glutamic acid monohydrate, DL-Alanine, Glycine, DL-Serine and DL-Lysine monohydrochloride). Morpheus condition H11 with 1mM TEW and 0.05 mg/mL Trypsin
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.302 α = 90 b = 91.302 β = 90 c = 323.657 γ = 90
Symmetry Space Group P 43 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 2025-01-25 M SINGLE WAVELENGTH 2 2 99 PIXEL DECTRIS EIGER2 XE 16M 2025-01-25
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04 2 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.28 80.91 100 0.447 0.064 1 9.3 48.6 44114 124.45
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 3.28 3.54 100 1.367 0.522 1.1 38.9
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 3.28 79.52 1.33 39965 1944 99.76 0.2114 0.2096 0.2103 0.2469 0.2493 130.14
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 5.007 f_angle_d 0.6194 f_chiral_restr 0.0427 f_plane_restr 0.0103 f_bond_d 0.0024
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6947 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 395
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling AutoSol phasing PHASER phasing