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EAL domain of phosphodiesterase PdeA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1M Bis Tris propane, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.193 α = 90 b = 46.963 β = 96.32 c = 63.77 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 MARMOSAIC 300 mm CCD MIRROR 2011-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
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 1.34 39.91 97.1 0.083 28.3 3.7 48723 48723 -3 10.42
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 1.34 1.36 90 0.37 2.8 2.9 2243
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 1.34 39.91 46411 46411 2476 97.3 0.1691 0.16761 0.167 0.19816 0.1981 RANDOM 9.423
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] -0.13 -0.53 -0.08 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.3 r_dihedral_angle_3_deg 12.351 r_dihedral_angle_4_deg 10.495 r_dihedral_angle_1_deg 6.127 r_scangle_it 4.549 r_scbond_it 2.838 r_mcangle_it 1.741 r_angle_refined_deg 1.648 r_mcbond_it 0.973 r_angle_other_deg 0.929
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.3 r_dihedral_angle_3_deg 12.351 r_dihedral_angle_4_deg 10.495 r_dihedral_angle_1_deg 6.127 r_scangle_it 4.549 r_scbond_it 2.838 r_mcangle_it 1.741 r_angle_refined_deg 1.648 r_mcbond_it 0.973 r_angle_other_deg 0.929 r_mcbond_other 0.291 r_chiral_restr 0.096 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 1952 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 2
Software Software Software Name Purpose Blu-Ice data collection HKL-3000 phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling