7Q9Q

Crystal structure of PDE6D Geranylgeranylated cystein complex


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP27730% w/v PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.1342.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.048α = 77.725
b = 35.289β = 68.98
c = 37.645γ = 69.228
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2019-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6A1NSLSX6A

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
11.4534.97195.9117.983.524436
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)
11.451.490.669

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-VALUE5TB51.4534.97124436122296.1930.2280.22510.273629.697
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]
-1.5460.939-0.1110.583-0.5921.126
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.333
r_dihedral_angle_3_deg15.033
r_dihedral_angle_4_deg8.193
r_dihedral_angle_1_deg6.659
r_lrange_it6.14
r_lrange_other6.117
r_scangle_it4.751
r_scangle_other4.749
r_mcangle_it3.376
r_mcangle_other3.376
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.333
r_dihedral_angle_3_deg15.033
r_dihedral_angle_4_deg8.193
r_dihedral_angle_1_deg6.659
r_lrange_it6.14
r_lrange_other6.117
r_scangle_it4.751
r_scangle_other4.749
r_mcangle_it3.376
r_mcangle_other3.376
r_scbond_it3.228
r_scbond_other3.226
r_mcbond_it2.478
r_mcbond_other2.474
r_angle_refined_deg1.839
r_angle_other_deg1.663
r_symmetry_xyhbond_nbd_other0.244
r_symmetry_nbd_other0.212
r_nbd_refined0.205
r_nbd_other0.193
r_xyhbond_nbd_refined0.182
r_nbtor_refined0.172
r_symmetry_xyhbond_nbd_refined0.146
r_symmetry_nbd_refined0.131
r_symmetry_nbtor_other0.084
r_chiral_restr0.083
r_gen_planes_refined0.012
r_gen_planes_other0.009
r_bond_refined_d
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1208
Nucleic Acid Atoms
Solvent Atoms115
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing