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hPDE2A catalytic domain complexed with IBMX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 Reservoir: 25% PEG 3350, 0.1M Tris pH8.5, 0.2M MgCl2
Protein: 25mM HEPES pH 7.5, 25mM NaCl, 2mM TCEP, 10ug/ml E-64, 1ug/ml pepstatin, 1mM IBMX, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.19 43.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.815 α = 109.3 b = 73.287 β = 88.8 c = 91.532 γ = 89
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 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.00 APS 23-ID-B
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 1.58 50 83.9 0.11 8.8 2.7 157174 -3
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) 1.58 1.64 36.7 0.338 1.2 6904
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.58 50 157107 7854 83.76 0.177 0.174 0.1717 0.233 0.2306 RANDOM 22.692
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] -0.04 0.03 0.75 -0.23 -0.07 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.976 r_dihedral_angle_4_deg 17.766 r_dihedral_angle_3_deg 14.675 r_scangle_it 5.708 r_dihedral_angle_1_deg 5.501 r_scbond_it 4.108 r_mcangle_it 2.431 r_angle_refined_deg 2.249 r_mcbond_it 1.712 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.976 r_dihedral_angle_4_deg 17.766 r_dihedral_angle_3_deg 14.675 r_scangle_it 5.708 r_dihedral_angle_1_deg 5.501 r_scbond_it 4.108 r_mcangle_it 2.431 r_angle_refined_deg 2.249 r_mcbond_it 1.712 r_nbtor_refined 0.317 r_nbd_refined 0.239 r_symmetry_hbond_refined 0.209 r_symmetry_vdw_refined 0.196 r_xyhbond_nbd_refined 0.186 r_chiral_restr 0.165 r_bond_refined_d 0.029 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10851 Nucleic Acid Atoms Solvent Atoms 1777 Heterogen Atoms 72
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction