5ZK5

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 DROP6.529530%(w/v) PEG6000, 0.1M Na-Hepes pH 6.5
Crystal Properties
Matthews coefficientSolvent content
1.9235.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.48α = 90
b = 65.09β = 90
c = 76.39γ = 90
Symmetry
Space GroupP 21 21 21

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 ID290.983998ESRFID29

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
11.595099.40.07916.118.79319
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)
11.591.680.4643.13

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 REPLACEMENTTHROUGHOUT4TPW2.2550882746599.390.201760.198260.26839RANDOM36.924
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]
3.21-2.81-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.62
r_dihedral_angle_3_deg15.725
r_dihedral_angle_4_deg13.541
r_dihedral_angle_1_deg6.929
r_long_range_B_refined5.22
r_long_range_B_other5.217
r_scangle_other3.614
r_mcangle_it3.105
r_mcangle_other3.102
r_scbond_it2.264
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.62
r_dihedral_angle_3_deg15.725
r_dihedral_angle_4_deg13.541
r_dihedral_angle_1_deg6.929
r_long_range_B_refined5.22
r_long_range_B_other5.217
r_scangle_other3.614
r_mcangle_it3.105
r_mcangle_other3.102
r_scbond_it2.264
r_scbond_other2.263
r_mcbond_it1.941
r_mcbond_other1.936
r_angle_refined_deg1.748
r_angle_other_deg1.295
r_chiral_restr0.082
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms1623
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing