7QJK

Crystal structure of PDE6D in complex with Compound-2


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2911.2 M AmSO4 and 0.1 M ammonium acetate pH 4.9 at 291K
Crystal Properties
Matthews coefficientSolvent content
2.5651.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.548α = 90
b = 76.548β = 90
c = 238.018γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97951DiamondI04

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
13.176.5590.60.9755.6812108
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)
13.13.310.343

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-VALUE5TB53.164.4631209562588.8290.2480.24640.283176.627
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]
-0.979-0.9791.958
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.758
r_dihedral_angle_3_deg19.209
r_dihedral_angle_4_deg17.759
r_lrange_it10.666
r_lrange_other10.665
r_scangle_it7.244
r_scangle_other7.242
r_mcangle_it6.668
r_mcangle_other6.667
r_dihedral_angle_1_deg5.988
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.758
r_dihedral_angle_3_deg19.209
r_dihedral_angle_4_deg17.759
r_lrange_it10.666
r_lrange_other10.665
r_scangle_it7.244
r_scangle_other7.242
r_mcangle_it6.668
r_mcangle_other6.667
r_dihedral_angle_1_deg5.988
r_scbond_it4.284
r_scbond_other4.282
r_mcbond_it4.159
r_mcbond_other4.153
r_chiral_restr_other2.517
r_angle_other_deg1.105
r_angle_refined_deg1.091
r_nbd_other0.307
r_symmetry_nbd_refined0.306
r_symmetry_nbd_other0.221
r_ncsr_local_group_60.213
r_ncsr_local_group_50.212
r_nbd_refined0.209
r_ncsr_local_group_30.209
r_symmetry_xyhbond_nbd_refined0.208
r_ncsr_local_group_40.182
r_ncsr_local_group_20.181
r_ncsr_local_group_10.178
r_nbtor_refined0.171
r_xyhbond_nbd_refined0.17
r_symmetry_nbtor_other0.076
r_symmetry_xyhbond_nbd_other0.054
r_chiral_restr0.034
r_bond_refined_d0.002
r_bond_other_d0.002
r_gen_planes_refined0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4674
Nucleic Acid Atoms
Solvent Atoms26
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing