5ZML

Stapled-peptides tailored against initiation of translation


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29540%(v/v) Ethylene glycol, 20 %(w/v) PEG 8000, 0.3M Sodium nitrate, 0.3M Ammonium sulfate, 100mM Sodium HEPES/MOPS pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.4650.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.29α = 90
b = 91.61β = 90
c = 136.83γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2016-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
11.868.4298.30.08813.056.122468
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)
11.81.8595.70.4513.17

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 REPLACEMENTTHROUGHOUT4BEA1.868.4220343208898.260.188250.184710.22259RANDOM26.189
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]
2.64-0.54-2.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.497
r_dihedral_angle_4_deg13.355
r_dihedral_angle_3_deg11.882
r_dihedral_angle_1_deg6.535
r_long_range_B_refined4.666
r_long_range_B_other4.665
r_scangle_other2.906
r_mcangle_it2.548
r_mcangle_other2.547
r_scbond_it1.798
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.497
r_dihedral_angle_4_deg13.355
r_dihedral_angle_3_deg11.882
r_dihedral_angle_1_deg6.535
r_long_range_B_refined4.666
r_long_range_B_other4.665
r_scangle_other2.906
r_mcangle_it2.548
r_mcangle_other2.547
r_scbond_it1.798
r_scbond_other1.796
r_mcbond_it1.585
r_mcbond_other1.574
r_angle_refined_deg1.423
r_angle_other_deg0.938
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms1683
Nucleic Acid Atoms
Solvent Atoms190
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing