7QF9

Crystal structure of PDE6D bound to HRas peptide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2910.1 M Tris pH 8.5, 8% w/v PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.2745.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.626α = 90
b = 82.789β = 90
c = 112.467γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-09-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.9556.23499.8116.96.424377
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)
11.9520.772

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-VALUE5TB51.9556.23424329119799.750.2330.22950.299341.591
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]
-0.5432.041-1.499
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.034
r_dihedral_angle_3_deg17.526
r_dihedral_angle_4_deg15.96
r_lrange_it7.551
r_lrange_other7.547
r_dihedral_angle_1_deg7.101
r_scangle_it5.633
r_scangle_other5.631
r_mcangle_it4.318
r_mcangle_other4.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.034
r_dihedral_angle_3_deg17.526
r_dihedral_angle_4_deg15.96
r_lrange_it7.551
r_lrange_other7.547
r_dihedral_angle_1_deg7.101
r_scangle_it5.633
r_scangle_other5.631
r_mcangle_it4.318
r_mcangle_other4.316
r_scbond_it3.822
r_scbond_other3.821
r_mcbond_it3.359
r_mcbond_other3.359
r_angle_other_deg1.538
r_angle_refined_deg1.165
r_symmetry_nbd_other0.222
r_nbd_other0.212
r_nbd_refined0.181
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.16
r_symmetry_xyhbond_nbd_refined0.144
r_ncsr_local_group_10.138
r_symmetry_nbd_refined0.133
r_symmetry_nbtor_other0.087
r_chiral_restr0.04
r_xyhbond_nbd_other0.039
r_symmetry_xyhbond_nbd_other0.01
r_bond_other_d0.003
r_bond_refined_d0.002
r_gen_planes_refined0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2440
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing