5B4K

Crystal structure of the catalytic domain of human PDE10A complexed with N-(4-((5-methyl-5H-pyrrolo[3,2-d]pyrimidin-4-yl)oxy)phenyl)-1H-benzimidazol-2-amine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277100 mM HEPES pH 7.6, 100 mM magnesium chloride hexahydrate, 24.182% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1141.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.734α = 90
b = 81.683β = 90
c = 161.654γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0000ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.980.8390.918.3613970
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.92.97

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3WYM2.980.831319168190.840.18080.176840.26051RANDOM56.224
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]
3.54-5.131.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.266
r_dihedral_angle_3_deg14.08
r_dihedral_angle_4_deg13.173
r_long_range_B_refined8.218
r_mcangle_it4.554
r_dihedral_angle_1_deg4.022
r_scbond_it3.749
r_mcbond_it2.836
r_angle_refined_deg0.914
r_chiral_restr0.059
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.266
r_dihedral_angle_3_deg14.08
r_dihedral_angle_4_deg13.173
r_long_range_B_refined8.218
r_mcangle_it4.554
r_dihedral_angle_1_deg4.022
r_scbond_it3.749
r_mcbond_it2.836
r_angle_refined_deg0.914
r_chiral_restr0.059
r_bond_refined_d0.004
r_gen_planes_refined0.004
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_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5129
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
MOLREPphasing
Cootmodel building