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Exploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ATW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.2 M tri-Potassium Citrate, 20% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 1.67 26.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 22.498 α = 90 b = 26.35 β = 90 c = 47.738 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN 944+ 2016-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.81 50 86 0.057 0.064 0.988 33 5.4 2451
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 1.81 1.875 15.6 0.95
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 6ATW 1.81 23.87 2339 114 85.68 0.175 0.1734 0.1825 0.212 0.218 RANDOM 13.514
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] -0.64 0.9 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.11 r_dihedral_angle_4_deg 27.127 r_dihedral_angle_3_deg 14.708 r_dihedral_angle_1_deg 7.129 r_angle_refined_deg 1.855 r_angle_other_deg 1.166 r_chiral_restr 0.118 r_bond_refined_d 0.018 r_bond_other_d 0.008 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.11 r_dihedral_angle_4_deg 27.127 r_dihedral_angle_3_deg 14.708 r_dihedral_angle_1_deg 7.129 r_angle_refined_deg 1.855 r_angle_other_deg 1.166 r_chiral_restr 0.118 r_bond_refined_d 0.018 r_bond_other_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 276 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction