7Q9S

Crystal structure of PDE6D KRas peptide complex with Compound-1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TB5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2910.2 M Lithium sulphate, 0.1M Tris pH 8.5 and 20% PEG 3000
Crystal Properties
Matthews coefficientSolvent content
2.6152.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.104α = 90
b = 81.123β = 90
c = 118.514γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.8540.6571000.9998.48.432070
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.90.88

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5TB51.8540.65732034157599.9060.2010.19930.227331.262
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]
0.019-0.2260.207
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.833
r_dihedral_angle_3_deg16.996
r_dihedral_angle_4_deg16.271
r_lrange_it8.79
r_lrange_other8.789
r_dihedral_angle_1_deg6.885
r_scangle_it6.561
r_scangle_other6.56
r_scbond_it4.319
r_scbond_other4.318
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.833
r_dihedral_angle_3_deg16.996
r_dihedral_angle_4_deg16.271
r_lrange_it8.79
r_lrange_other8.789
r_dihedral_angle_1_deg6.885
r_scangle_it6.561
r_scangle_other6.56
r_scbond_it4.319
r_scbond_other4.318
r_mcangle_it3.825
r_mcangle_other3.824
r_mcbond_it2.893
r_mcbond_other2.892
r_angle_other_deg1.434
r_angle_refined_deg1.379
r_nbd_refined0.498
r_symmetry_xyhbond_nbd_other0.388
r_xyhbond_nbd_refined0.306
r_symmetry_nbd_other0.297
r_nbd_other0.289
r_symmetry_nbd_refined0.228
r_nbtor_refined0.173
r_symmetry_xyhbond_nbd_refined0.122
r_symmetry_nbtor_other0.095
r_chiral_restr0.054
r_chiral_restr_other0.006
r_bond_refined_d0.004
r_bond_other_d0.004
r_gen_planes_refined0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2489
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms113

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing