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X-RAY STRUCTURE OF PDE9A IN COMPLEX WITH Inhibitor 13A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other inhouse structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 35% PP 5/4, 0.2 M KCl, 50 mM Hepes pH 7.25
Crystal Properties Matthews coefficient Solvent content 5 75.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 222.423 α = 90 b = 222.423 β = 90 c = 120.257 γ = 90
Symmetry Space Group I 4 2 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 PIXEL DECTRIS PILATUS 6M 2015-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 3.3 50 99.6 0.998 12.1 8.8 22982
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.49 0.739
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 inhouse structure 3.3 49.74 21832 1149 99.59 0.24974 0.24649 0.2557 0.31232 0.3143 RANDOM 131.928
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] 4.01 4.01 -8.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.885 r_dihedral_angle_3_deg 16.146 r_mcangle_it 15.42 r_mcangle_other 15.417 r_dihedral_angle_4_deg 14.198 r_scangle_other 13.002 r_mcbond_other 9.765 r_mcbond_it 9.763 r_scbond_it 8.043 r_scbond_other 8.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.885 r_dihedral_angle_3_deg 16.146 r_mcangle_it 15.42 r_mcangle_other 15.417 r_dihedral_angle_4_deg 14.198 r_scangle_other 13.002 r_mcbond_other 9.765 r_mcbond_it 9.763 r_scbond_it 8.043 r_scbond_other 8.042 r_dihedral_angle_1_deg 7.051 r_angle_refined_deg 1.563 r_angle_other_deg 1.019 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 5160 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing