9JDU | pdb_00009jdu

The crystal structure of PDE10A complexed with inhibitor 2061


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OUP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2770.1M Hepes (pH 7.5), 0.2M MgCl2, 18-20% PEG 3350, 50mM 2-mercaptoethanol
Crystal Properties
Matthews coefficientSolvent content
2.1743.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.509α = 90
b = 81.583β = 90
c = 159.744γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-30002022-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
12.323.8499.560.1417.39.72950228.1337719316
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.381000.472.87.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTNONE2OUP2.300017511823.83532191.3604088318229466150599.67188715620.2478212318110.2450646359590.25340.2972103124630.305535.4768196451
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.9697569447
f_angle_d0.53297136036
f_chiral_restr0.0370022053428
f_plane_restr0.00418631441433
f_bond_d0.00248743170165
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5212
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
CrysalisProdata reduction
PHASERphasing