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VEALYL peptide derived from human insulin chain B, residues 12-17
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other polyalanine beta strands with ideal geometry
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 2.5 310 2mM peptide in 100 mM NaCl and 50 mM phosphate. Crystals can be more easily reproduced by dissolving peptide to 2 mM in water at room temperature, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 18.425 α = 90.88 b = 9.613 β = 96.12 c = 21.975 γ = 100.93
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 MAR CCD 165 mm 2005-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID13 ESRF ID13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 90 93 0.172 3.9 820 17.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.83 91.7 0.413 299
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 polyalanine beta strands with ideal geometry 2 21.84 820 40 83.25 0.205 0.201 0.2023 0.265 0.2547 RANDOM 18.338
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] 2.14 0.41 0.99 0.34 -0.09 -2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.309 r_dihedral_angle_3_deg 13.076 r_scangle_it 10.186 r_dihedral_angle_1_deg 7.878 r_scbond_it 7.371 r_mcangle_it 6.952 r_mcbond_it 5.574 r_angle_other_deg 3.119 r_angle_refined_deg 2.271 r_xyhbond_nbd_refined 0.287
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.309 r_dihedral_angle_3_deg 13.076 r_scangle_it 10.186 r_dihedral_angle_1_deg 7.878 r_scbond_it 7.371 r_mcangle_it 6.952 r_mcbond_it 5.574 r_angle_other_deg 3.119 r_angle_refined_deg 2.271 r_xyhbond_nbd_refined 0.287 r_nbd_other 0.253 r_symmetry_vdw_other 0.227 r_nbd_refined 0.224 r_nbtor_refined 0.214 r_symmetry_vdw_refined 0.204 r_symmetry_hbond_refined 0.192 r_nbtor_other 0.136 r_chiral_restr 0.036 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_gen_planes_other 0.002 r_bond_other_d r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 200 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction