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human phosphodiestrase 9 in complex with cGMP (Zn inhibited)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TBM
Crystallization Crystal Properties Matthews coefficient Solvent content 4.69 73.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.857 α = 90 b = 103.857 β = 90 c = 270.118 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 CCD ADSC QUANTUM 210 2006-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 2.1 50 99.82 0.09 18.1 6.1 87053 77963 2 37.9
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 FOURIER SYNTHESIS THROUGHOUT 1TBM 2.1 50 77963 8759 99.82 0.18251 0.18017 0.1882 0.20274 0.2117 RANDOM 31.797
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] 1.49 1.49 -2.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.403 r_dihedral_angle_4_deg 20.959 r_dihedral_angle_3_deg 16.63 r_dihedral_angle_1_deg 6.147 r_scangle_it 6.133 r_scbond_it 4.262 r_mcangle_it 2.362 r_mcbond_it 2.171 r_angle_refined_deg 1.12 r_angle_other_deg 0.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.403 r_dihedral_angle_4_deg 20.959 r_dihedral_angle_3_deg 16.63 r_dihedral_angle_1_deg 6.147 r_scangle_it 6.133 r_scbond_it 4.262 r_mcangle_it 2.362 r_mcbond_it 2.171 r_angle_refined_deg 1.12 r_angle_other_deg 0.807 r_mcbond_other 0.44 r_symmetry_vdw_refined 0.294 r_symmetry_vdw_other 0.24 r_nbd_refined 0.238 r_nbd_other 0.217 r_xyhbond_nbd_refined 0.205 r_symmetry_hbond_refined 0.202 r_nbtor_refined 0.192 r_nbtor_other 0.091 r_chiral_restr 0.077 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5412 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement