3ZRM | pdb_00003zrm

Identification of 2-(4-pyridyl)thienopyridinones as GSK-3beta inhibitors


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GNGPDB ENTRY 1GNG

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.5651.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.08α = 90
b = 153.08β = 90
c = 200.873γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
12.49401000.124.27.431863
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)
12.492.531000.495.17.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1GNG2.492030492129699.920.190280.187960.190.246580.24RANDOM41.067
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]
-0.32-0.16-0.320.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.648
r_dihedral_angle_4_deg22.43
r_dihedral_angle_3_deg16.847
r_dihedral_angle_1_deg5.554
r_scangle_it4.583
r_scbond_it3.079
r_mcangle_it2.22
r_angle_refined_deg1.203
r_mcbond_it1.111
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.648
r_dihedral_angle_4_deg22.43
r_dihedral_angle_3_deg16.847
r_dihedral_angle_1_deg5.554
r_scangle_it4.583
r_scbond_it3.079
r_mcangle_it2.22
r_angle_refined_deg1.203
r_mcbond_it1.111
r_nbtor_refined0.307
r_symmetry_vdw_refined0.224
r_nbd_refined0.201
r_symmetry_hbond_refined0.15
r_xyhbond_nbd_refined0.13
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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_other
r_long_range_B_refined
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 Atoms5902
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling