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Lybatide 2, a cystine-rich peptide from Lycium barbarum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 1.6 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, pH 4.5,
2% PEG400
Crystal Properties Matthews coefficient Solvent content 2.02 39.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 19.318 α = 90 b = 54.655 β = 100.6 c = 42.4 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M-F 2015-07-24 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.9184, 1.8000 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.48 41.68 99.6 0.033 0.014 0.999 44.3 6.5 14465
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 1.48 1.56 98.4 0.039 0.017 0.998 31.8 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.48 41.68 13735 713 99.48 0.10904 0.1076 0.1076 0.137 0.1361 RANDOM 10.561
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] 0.06 0.11 0.06 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.96 r_dihedral_angle_3_deg 10.035 r_long_range_B_refined 7.297 r_long_range_B_other 7.293 r_dihedral_angle_1_deg 6.585 r_dihedral_angle_4_deg 6.125 r_scangle_other 2.588 r_angle_refined_deg 1.951 r_scbond_it 1.823 r_scbond_other 1.821
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.96 r_dihedral_angle_3_deg 10.035 r_long_range_B_refined 7.297 r_long_range_B_other 7.293 r_dihedral_angle_1_deg 6.585 r_dihedral_angle_4_deg 6.125 r_scangle_other 2.588 r_angle_refined_deg 1.951 r_scbond_it 1.823 r_scbond_other 1.821 r_mcangle_other 1.371 r_mcangle_it 1.368 r_angle_other_deg 1.237 r_mcbond_it 0.88 r_mcbond_other 0.854 r_chiral_restr 0.145 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 728 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling SHELXDE phasing