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The structure of human PDE12 residues 161-609 in complex with GSK3036342A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NG0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 0.1M Tris Ph 8.5
15% Peg20000
25% Ethylene Glycol
Crystal Properties Matthews coefficient Solvent content 2.32 47.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.309 α = 90 b = 66.532 β = 90 c = 124.88 γ = 90
Symmetry Space Group P 21 21 21
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 RIGAKU SATURN 944+ 2012-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
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 1.8 50 91.9 0.054 15.2 4.8 40745 20.62
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 66.1 0.266 0.332 0.195 0.904 2.1 1437
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 3NG0 1.8 27.3 39837 1255 89.99 0.1827 0.1815 0.1781 0.2181 0.2192 RANDOM 21.79
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] -0.4148 0.1225 0.2923
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.99 t_other_torsion 2.52 t_angle_deg 0.98 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.99 t_other_torsion 2.52 t_angle_deg 0.98 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 3579 Nucleic Acid Atoms Solvent Atoms 462 Heterogen Atoms 59
Software Software Software Name Purpose BUSTER refinement HKL-2000 data collection SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction