7Q9U

Crystal structure of the high affinity KRas mutant PDE6D complex


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 Ammonium sulphate, 0.1 M tri sodium citrate pH 5.6, 15 % w/v PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.8857.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.086α = 82.771
b = 57.925β = 81.709
c = 78.913γ = 68.447
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97628DiamondI03

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
12.23853.70694.70.9956.11.737781
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)
12.242.30.742

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-VALUE5TB52.23853.70637435177493.4960.2020.19940.254546.809
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]
-0.621-0.994-0.9330.4690.805-0.876
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.168
r_dihedral_angle_4_deg18.934
r_dihedral_angle_3_deg18.179
r_lrange_it9.087
r_lrange_other9.086
r_scangle_it7.043
r_scangle_other7.042
r_dihedral_angle_1_deg6.981
r_mcangle_it5.402
r_mcangle_other5.401
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.168
r_dihedral_angle_4_deg18.934
r_dihedral_angle_3_deg18.179
r_lrange_it9.087
r_lrange_other9.086
r_scangle_it7.043
r_scangle_other7.042
r_dihedral_angle_1_deg6.981
r_mcangle_it5.402
r_mcangle_other5.401
r_scbond_it4.566
r_scbond_other4.566
r_mcbond_it3.676
r_mcbond_other3.676
r_angle_refined_deg1.609
r_angle_other_deg1.341
r_symmetry_xyhbond_nbd_refined0.251
r_symmetry_nbd_refined0.25
r_nbd_other0.248
r_nbd_refined0.2
r_symmetry_nbd_other0.198
r_xyhbond_nbd_refined0.175
r_nbtor_refined0.159
r_ncsr_local_group_10.097
r_symmetry_nbtor_other0.083
r_ncsr_local_group_20.076
r_chiral_restr0.073
r_symmetry_xyhbond_nbd_other0.033
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.003
r_bond_refined_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5140
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms137

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing