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PDE7A catalytic domain in complex with 2-(Cyclopentylamino)thieno[3,2-d]pyrimidin-4(3H)-one derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZKL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.6 - 0.8M (NH4)2SO4, 3mM mercaptoethanol, 10mM MgCl2, 10mM EDTA, 0.1M Tris HCl, pH 7.5,
Crystal Properties Matthews coefficient Solvent content 3.08 60.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.187 α = 90 b = 116.187 β = 90 c = 64.458 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS VII 2011-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.9
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 29.75 94.3 35.7 8.4 29559
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1ZKL 2.1 29.75 25982 1417 92.8 0.17443 0.1721 0.1725 0.21763 0.2169 RANDOM 31.804
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] 0.05 0.02 0.05 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.371 r_dihedral_angle_4_deg 25.275 r_dihedral_angle_3_deg 15.174 r_dihedral_angle_1_deg 5.77 r_scangle_it 5.428 r_scbond_it 3.553 r_mcangle_it 2.104 r_angle_refined_deg 1.757 r_mcbond_it 1.156 r_chiral_restr 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.371 r_dihedral_angle_4_deg 25.275 r_dihedral_angle_3_deg 15.174 r_dihedral_angle_1_deg 5.77 r_scangle_it 5.428 r_scbond_it 3.553 r_mcangle_it 2.104 r_angle_refined_deg 1.757 r_mcbond_it 1.156 r_chiral_restr 0.135 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 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 Atoms Number Protein Atoms 2595 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement