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HelloH-GGFF - A de novo peptide with tertiary structure.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8VPD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SLOW COOLING 298 Acetonitrile, water
Crystal Properties Matthews coefficient Solvent content 1.62 23.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.169 α = 90 b = 8.896 β = 115.8 c = 34.708 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER X 9M 2023-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.619900 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 0.91 17.18 97.92 0.999 30.49 6.6 7774 4
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 0.91 0.9425 0.992
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 0.91 17.18 1.37 7774 1438 97.55 0.0638 0.0633 0.0633 0.0687 0.0686 5.48
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 22.7351 f_angle_d 1.7108 f_chiral_restr 0.0773 f_bond_d 0.0079 f_plane_restr 0.0062
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 117 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing