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Crystal structure of the human Phosphodiesterase 9A catalytic domain complexed with IBMX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TBM PDB ENTRY 1TBM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 2mM IBMX, 0.1 M Hepes, 2.2M Na-formate, 3% xylitol, 20mM ZnSO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.69 73.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.27 α = 90 b = 104.27 β = 90 c = 269.61 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 IMAGE PLATE RIGAKU RAXIS V mirrors 2006-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.8 50 99 0.11 13.1 6.5 37083 -3 50.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.9 98 0.39 2.5
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 PDB ENTRY 1TBM 2.8 45.95 37054 1856 98.9 0.206 0.206 0.207 0.24 0.2031 RANDOM 41.9
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] 4.48 4.48 -8.95
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.1 c_scangle_it 2.84 c_mcangle_it 1.95 c_scbond_it 1.78 c_angle_deg 1.2 c_mcbond_it 1.13 c_improper_angle_d 0.79 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.1 c_scangle_it 2.84 c_mcangle_it 1.95 c_scbond_it 1.78 c_angle_deg 1.2 c_mcbond_it 1.13 c_improper_angle_d 0.79 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5371 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 36
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing