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PDE2a catalytic domain in complex with a brain penetrant inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other INTERNAL PDE2A MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 0.2 M MGCL2, 0.1 M TRIS-HCL PH 7.0 AND 20 % PEG 3350 IN PRESENCE OF 1 MM LIGAND
Crystal Properties Matthews coefficient Solvent content 2.3 46.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.14 α = 109.37 b = 73.43 β = 91.82 c = 91.62 γ = 91.05
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN 944 VARIAMAXHF 2009-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 30 93.7 0.1 5.8 1.9 44706 1.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 85.4 0.38 1.8 1.9
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 INTERNAL PDE2A MODEL 2.5 19.77 42432 2266 93.67 0.21004 0.20642 0.211 0.27746 0.281 RANDOM 30.798
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] 0.1 -0.1 -0.11 -0.19 -0.02 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.908 r_dihedral_angle_4_deg 15.553 r_dihedral_angle_3_deg 15.292 r_dihedral_angle_1_deg 5.213 r_long_range_B_refined 3.308 r_long_range_B_other 3.295 r_mcangle_it 1.704 r_mcangle_other 1.704 r_scangle_other 1.665 r_angle_refined_deg 1.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.908 r_dihedral_angle_4_deg 15.553 r_dihedral_angle_3_deg 15.292 r_dihedral_angle_1_deg 5.213 r_long_range_B_refined 3.308 r_long_range_B_other 3.295 r_mcangle_it 1.704 r_mcangle_other 1.704 r_scangle_other 1.665 r_angle_refined_deg 1.004 r_mcbond_it 0.996 r_mcbond_other 0.995 r_scbond_it 0.96 r_scbond_other 0.96 r_angle_other_deg 0.755 r_chiral_restr 0.056 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10725 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing