4PM0

PDE7A catalytic domain in complex with 2-(Cyclopentylamino)thieno[3,2-d]pyrimidin-4(3H)-one derivative


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZKL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.6 - 0.8M (NH4)2SO4, 3mM mercaptoethanol, 10mM MgCl2, 10mM EDTA, 0.1M Tris HCl, pH 7.5,
Crystal Properties
Matthews coefficientSolvent content
3.0860.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.187α = 90
b = 116.187β = 90
c = 64.458γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS VII2011-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.9

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
12.129.7594.335.78.429559

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 REPLACEMENTTHROUGHOUT1ZKL2.129.7525982141792.80.174430.17210.21763RANDOM31.804
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]
0.050.020.05-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.371
r_dihedral_angle_4_deg25.275
r_dihedral_angle_3_deg15.174
r_dihedral_angle_1_deg5.77
r_scangle_it5.428
r_scbond_it3.553
r_mcangle_it2.104
r_angle_refined_deg1.757
r_mcbond_it1.156
r_chiral_restr0.135
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.371
r_dihedral_angle_4_deg25.275
r_dihedral_angle_3_deg15.174
r_dihedral_angle_1_deg5.77
r_scangle_it5.428
r_scbond_it3.553
r_mcangle_it2.104
r_angle_refined_deg1.757
r_mcbond_it1.156
r_chiral_restr0.135
r_bond_refined_d0.024
r_gen_planes_refined0.01
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_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 Atoms2595
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement