5NGN

Lybatide 2, a cystine-rich peptide from Lycium barbarum


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2911.6 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, pH 4.5, 2% PEG400
Crystal Properties
Matthews coefficientSolvent content
2.0239.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 19.318α = 90
b = 54.655β = 100.6
c = 42.4γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-07-24MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P110.9184, 1.8000PETRA III, DESYP11

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.4841.6899.60.0330.0140.99944.36.514465
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)RedundancyNumber Unique Reflections (All)
11.481.5698.40.0390.0170.99831.86.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.4841.681373571399.480.109040.10760.137RANDOM10.561
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]
0.060.110.06-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.96
r_dihedral_angle_3_deg10.035
r_long_range_B_refined7.297
r_long_range_B_other7.293
r_dihedral_angle_1_deg6.585
r_dihedral_angle_4_deg6.125
r_scangle_other2.588
r_angle_refined_deg1.951
r_scbond_it1.823
r_scbond_other1.821
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.96
r_dihedral_angle_3_deg10.035
r_long_range_B_refined7.297
r_long_range_B_other7.293
r_dihedral_angle_1_deg6.585
r_dihedral_angle_4_deg6.125
r_scangle_other2.588
r_angle_refined_deg1.951
r_scbond_it1.823
r_scbond_other1.821
r_mcangle_other1.371
r_mcangle_it1.368
r_angle_other_deg1.237
r_mcbond_it0.88
r_mcbond_other0.854
r_chiral_restr0.145
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms728
Nucleic Acid Atoms
Solvent Atoms155
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing