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Catalytic Domain Of Human Phosphodiesterase 4D In Complex With AMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 288 PEG 3000, ethylene glycol, isopropanol, glycerol, DTT, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.57 52.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.316 α = 90 b = 78.958 β = 90 c = 164.74 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 93 CCD ADSC QUANTUM 210 2003-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1 ALS 8.3.1
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 1.63 81.65 91.85 0.057 9 2.9 86294 86294
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 1.63 1.672 76.4 0.59 1.65 2.9 5428
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 (All) 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 1.63 81.65 86294 86294 4527 91.85 0.17991 0.17991 0.17927 0.201 0.19185 0.2099 RANDOM 8.999
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] 1.06 0.52 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 2.808 r_scangle_it 2.511 r_scbond_it 1.489 r_angle_refined_deg 1.152 r_angle_other_deg 0.805 r_mcangle_it 0.794 r_mcbond_it 0.399 r_symmetry_vdw_other 0.321 r_nbd_other 0.226 r_symmetry_vdw_refined 0.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 2.808 r_scangle_it 2.511 r_scbond_it 1.489 r_angle_refined_deg 1.152 r_angle_other_deg 0.805 r_mcangle_it 0.794 r_mcbond_it 0.399 r_symmetry_vdw_other 0.321 r_nbd_other 0.226 r_symmetry_vdw_refined 0.225 r_nbd_refined 0.212 r_symmetry_hbond_refined 0.198 r_xyhbond_nbd_refined 0.15 r_nbtor_other 0.081 r_chiral_restr 0.075 r_metal_ion_refined 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5246 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 177
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection ELVES data scaling EPMR phasing