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Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-48
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 4.6MG/ML VCID7620 + 0.5MM T-048-1
1MM DTT, 0.1MM ZNCL2, 0.1MM MGCL2 (BATCH 1214013) AGAINST
SPARSE MATRIX CONDITION MORPHEUS C4, 12.5% W/V PEG1,000 ,
12.5% W/V PEG3,350 , 12.5% W/V MPD , 0.03M NPS (SODIUM
NITRATE, DISODIUM HYDROGEN PHOSPHATE, AMMONIUM SULFATE), 0.1M
MES/IMIDAZOLE PH 6.5, CRYO-PROTECTED - DIRECT (QYM9-2), VAPOR
DIFFUSION, SITTING DROP, TEMPERATURE 289K
Crystal Properties Matthews coefficient Solvent content 2.15 42.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.64 α = 90 b = 82.07 β = 110.23 c = 116.53 γ = 90
Symmetry Space Group P 1 21 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 2012-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9786 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 2.15 50 97.6 0.085 11.59 3.2 76922 -3 34.64
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 2.15 2.21 98.4 0.504 2.6 3.2
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 2.15 19.91 76919 3879 98.4 0.174 0.172 0.1825 0.21 0.2186 RANDOM 27.97
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] 0.05 -1.55 1.14 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.93 r_dihedral_angle_4_deg 14.872 r_dihedral_angle_3_deg 14.035 r_dihedral_angle_1_deg 5.218 r_angle_refined_deg 1.552 r_angle_other_deg 1.244 r_chiral_restr 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.93 r_dihedral_angle_4_deg 14.872 r_dihedral_angle_3_deg 14.035 r_dihedral_angle_1_deg 5.218 r_angle_refined_deg 1.552 r_angle_other_deg 1.244 r_chiral_restr 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.008 r_gen_planes_other 0.008 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10489 Nucleic Acid Atoms Solvent Atoms 563 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling