4JVF

The Crystal structure of PDE6D in complex with the inhibitor (s)-5


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.429318% PEG 4000, 25mM Sodium Acetate, 200mM Ammonium Sulphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9958.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.91α = 90
b = 55.91β = 90
c = 116.67γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.427.9990.12286598659-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.598.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT3T5G2.427.9-38225822543399.040.209490.206970.25659RANDOM31.222
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]
1.460.731.46-2.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.363
r_dihedral_angle_3_deg18.107
r_dihedral_angle_4_deg17.629
r_dihedral_angle_1_deg7.743
r_angle_refined_deg1.98
r_chiral_restr0.123
r_bond_refined_d0.022
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.363
r_dihedral_angle_3_deg18.107
r_dihedral_angle_4_deg17.629
r_dihedral_angle_1_deg7.743
r_angle_refined_deg1.98
r_chiral_restr0.123
r_bond_refined_d0.022
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1158
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms48

Software

Software
Software NamePurpose
ProDCdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling