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Crystal Structure of a synthetic ABC heterotrimeric Collagen-like Peptide at 1.53 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T4F residues A:8-16, B:7-15, C:6-14 with Lys and Glu residues truncated at the C-beta position
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 25 % (w/v) Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.03 39.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.706 α = 109.42 b = 27.876 β = 111.8 c = 28.396 γ = 95.73
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 RIGAKU HyPix-Arc 150 2023-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU PhotonJet-S 1.54184
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 1.53 25.4 97.2 0.08 0.096 0.029 0.999 23.54 8.1 10535 10.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.53 1.59 73.5 0.448 0.665 0.331 0.714 2
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 3t4f 1.53 24.16 2 10513 521 97.27 0.1514 0.1497 0.1499 0.1852 0.1871 random 17.7
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 17.371 f_angle_d 0.94 f_chiral_restr 0.054 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 632 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement PHASER phasing Arcimboldo phasing CrysalisPro data scaling CrysalisPro data reduction