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Crystal structure of PDE9 in complex with racemic inhibitor C33
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 277 The PDE9A2 (8-10 mg/mL) in a buffer of 50 mM NaCl, 20 mM Tris-HCl, pH 7.5, 1 mM mercaptoethanol, and 1 mM EDTA was mixed with 2 mM C33 and crystallized against a well buffer of 1.8 - 2.0 M sodium formate.
Crystal Properties Matthews coefficient Solvent content 2.96 58.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.135 α = 90 b = 104.135 β = 90 c = 269.536 γ = 90
Symmetry Space Group P 41 21 2
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 ADSC QUANTUM 315 2014-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1 NSLS X29A
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 2 100 97.2 20.8 12.6 96827
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.01 97.14 92056 4732 97 0.22395 0.22276 0.2284 0.24725 0.2511 RANDOM 40.214
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] -0.04 -0.04 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.373 r_dihedral_angle_4_deg 17.777 r_dihedral_angle_3_deg 13.55 r_long_range_B_refined 4.979 r_long_range_B_other 4.944 r_dihedral_angle_1_deg 4.942 r_scangle_other 3.442 r_mcangle_it 2.619 r_mcangle_other 2.619 r_scbond_it 2.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.373 r_dihedral_angle_4_deg 17.777 r_dihedral_angle_3_deg 13.55 r_long_range_B_refined 4.979 r_long_range_B_other 4.944 r_dihedral_angle_1_deg 4.942 r_scangle_other 3.442 r_mcangle_it 2.619 r_mcangle_other 2.619 r_scbond_it 2.164 r_scbond_other 2.164 r_mcbond_it 1.609 r_mcbond_other 1.608 r_angle_refined_deg 1.067 r_angle_other_deg 0.792 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 5357 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing