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PDE2 catalytic domain complexed with inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ITU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 25% PEG 3350, 0.1 M Tris, pH 8.5, and 0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.21 44.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.256 α = 90 b = 74.369 β = 110.33 c = 91.641 γ = 90
Symmetry Space Group C 1 2 1
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 210 2006-06-19 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 1.75 40 99.8 0.075 9.5 3.6 106728 26.47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81 99.5 0.41 3.2 10590
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 3ITU 1.75 38.92 106093 5295 99.85 0.169 0.1676 0.1676 0.197 0.1955 RANDOM 32.7
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] 3.1959 5.7741 -2.7029 -0.493
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.93 t_omega_torsion 3.04 t_angle_deg 0.88 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.93 t_omega_torsion 3.04 t_angle_deg 0.88 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8231 Nucleic Acid Atoms Solvent Atoms 997 Heterogen Atoms 220
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling BUSTER refinement PDB_EXTRACT data extraction HKL-2000 data reduction REFMAC phasing DENZO data reduction