5ZK9

Stapled-peptides tailored against initiation of translation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4TPW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529512.5% pEG1000 w/v, 12.5% PEG3350 w/v, 12.5% MPD w/v, 0.1M MES/imidazole pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.448.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.42α = 90
b = 38.08β = 122.72
c = 78.49γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.983994ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
11.765098.60.04815.335.822709
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.761.860.4412.18

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4TPW1.7645.6521571113698.920.178810.177090.2115RANDOM23.414
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]
0.860.110.07-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.805
r_dihedral_angle_4_deg13.68
r_dihedral_angle_3_deg12.071
r_dihedral_angle_1_deg6.526
r_long_range_B_refined5.07
r_long_range_B_other5.069
r_scangle_other3.074
r_mcangle_other2.17
r_mcangle_it2.169
r_scbond_it1.966
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.805
r_dihedral_angle_4_deg13.68
r_dihedral_angle_3_deg12.071
r_dihedral_angle_1_deg6.526
r_long_range_B_refined5.07
r_long_range_B_other5.069
r_scangle_other3.074
r_mcangle_other2.17
r_mcangle_it2.169
r_scbond_it1.966
r_scbond_other1.964
r_angle_refined_deg1.684
r_angle_other_deg1.357
r_mcbond_it1.343
r_mcbond_other1.341
r_chiral_restr0.084
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.003
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 Atoms1639
Nucleic Acid Atoms
Solvent Atoms166
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing