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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 1SIS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 298 100 mM Na Acetate pH 4.5, 600 mM AmPO4
Crystal Properties Matthews coefficient Solvent content 2.27 45.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.437 α = 90 b = 41.437 β = 90 c = 88.093 γ = 90
Symmetry Space Group P 43 21 2
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 2015-07-02 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) Rpim I (All) 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 2.2 50 100 0.124 0.021 44.9 58.4 4317
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 100 0.348 0.049 0.993 26.7 59.5
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 1SIS 2.2 37.5 4048 231 99.93 0.17545 0.17217 0.1799 0.23558 0.2379 RANDOM 15.807
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] 0.13 0.13 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 26.111 r_dihedral_angle_2_deg 17.989 r_dihedral_angle_3_deg 13.68 r_dihedral_angle_1_deg 6.387 r_long_range_B_refined 4.628 r_long_range_B_other 4.134 r_angle_refined_deg 1.337 r_angle_other_deg 0.922 r_mcangle_it 0.861 r_mcangle_other 0.861
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 26.111 r_dihedral_angle_2_deg 17.989 r_dihedral_angle_3_deg 13.68 r_dihedral_angle_1_deg 6.387 r_long_range_B_refined 4.628 r_long_range_B_other 4.134 r_angle_refined_deg 1.337 r_angle_other_deg 0.922 r_mcangle_it 0.861 r_mcangle_other 0.861 r_mcbond_it 0.454 r_mcbond_other 0.453 r_scangle_other 0.386 r_scbond_other 0.184 r_scbond_it 0.183 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 556 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing