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human phosphodiestrase 9 (inhibited by omitting divalent cation) in complex with cGMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TBM PDB ENTRY 1TBM
Crystallization Crystal Properties Matthews coefficient Solvent content 4.66 73.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.65 α = 90 b = 103.65 β = 90 c = 270.041 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 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 2.3 50 98.7 0.085 23 7 65299 2
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 PDB ENTRY 1TBM 2.5 50 46414 5261 99.54 0.19885 0.19566 0.1992 0.22627 0.2259 RANDOM 40.023
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] 1.86 1.86 -3.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.991 r_dihedral_angle_4_deg 21.603 r_dihedral_angle_3_deg 17.57 r_dihedral_angle_1_deg 6.529 r_scangle_it 4.327 r_scbond_it 2.76 r_mcangle_it 1.499 r_angle_refined_deg 1.35 r_angle_other_deg 0.832 r_mcbond_it 0.717
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.991 r_dihedral_angle_4_deg 21.603 r_dihedral_angle_3_deg 17.57 r_dihedral_angle_1_deg 6.529 r_scangle_it 4.327 r_scbond_it 2.76 r_mcangle_it 1.499 r_angle_refined_deg 1.35 r_angle_other_deg 0.832 r_mcbond_it 0.717 r_symmetry_vdw_other 0.3 r_symmetry_vdw_refined 0.27 r_symmetry_hbond_refined 0.268 r_nbd_refined 0.262 r_nbd_other 0.213 r_xyhbond_nbd_refined 0.207 r_metal_ion_refined 0.203 r_nbtor_refined 0.201 r_mcbond_other 0.187 r_nbtor_other 0.092 r_chiral_restr 0.077 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_xyhbond_nbd_other 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 238 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement