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Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-49
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.14 289 5.0MG/ML VCID7620 + 0.5MM T-049
1MM DTT, 0.1MM ZNCL2, 0.1MM MGCL2 (BATCH 1214023) AGAINST
OPTIMIZATION MATRIX BASED ON CONDITION MORPHEUS C8, 47.47%V/V
OF 2X MORPHEUS-PPT4 (FINAL = 11.8% W/V PEG1,000 , 11.8% W/V
PEG3,350 , 11.8% W/V MPD), 0.03M NPS (SODIUM NITRATE, DISODIUM
HYDROGEN PHOSPHATE, AMMONIUM SULFATE), 0.1M HEPES PH 7.14,
CRYO-PROTECTED - DIRECT (ZQV4-6); TRAY ID 236552B5, VAPOR
DIFFUSION, SITTING DROP, TEMPERATURE 289K
Crystal Properties Matthews coefficient Solvent content 2.44 49.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.04 α = 90 b = 85.66 β = 110.41 c = 83.45 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 225 mm CCD 2012-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.45 50 97.9 0.046 20.27 3.3 29617 -3 56.07
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 2.45 2.51 99 0.504 2.5 3.3
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 2.45 42.87 29616 1504 99 0.187 0.184 0.1876 0.23 0.2227 RANDOM 50.86
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] 0.8 0.06 1.3 -1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.73 r_dihedral_angle_4_deg 23.778 r_dihedral_angle_3_deg 14.995 r_dihedral_angle_1_deg 5.21 r_angle_refined_deg 1.534 r_angle_other_deg 0.987 r_chiral_restr 0.079 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_gen_planes_other 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.73 r_dihedral_angle_4_deg 23.778 r_dihedral_angle_3_deg 14.995 r_dihedral_angle_1_deg 5.21 r_angle_refined_deg 1.534 r_angle_other_deg 0.987 r_chiral_restr 0.079 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.004 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 5210 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling