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Crystal structure of human phosphodiesterase 4d with regulatory domain and d155871
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 100MM HEPES PH 7.5, 100 MM NACL, 18% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 38.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.129 α = 90 b = 75.311 β = 92.43 c = 162.559 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
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 2.3 50 95 0.096 6.3 2.9 64589
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) 2.3 2.38 74.3 0.391 1.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.3 48.8 64569 3262 0.191 0.188 0.257 0.2328 RANDOM 22.14
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] 0.07 0.08 -0.14 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.681 r_dihedral_angle_4_deg 19.158 r_dihedral_angle_3_deg 17.179 r_dihedral_angle_1_deg 8.604 r_scangle_it 3.689 r_scbond_it 2.27 r_angle_refined_deg 1.39 r_mcangle_it 1.354 r_angle_other_deg 1.332 r_mcbond_it 0.683
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.681 r_dihedral_angle_4_deg 19.158 r_dihedral_angle_3_deg 17.179 r_dihedral_angle_1_deg 8.604 r_scangle_it 3.689 r_scbond_it 2.27 r_angle_refined_deg 1.39 r_mcangle_it 1.354 r_angle_other_deg 1.332 r_mcbond_it 0.683 r_mcbond_other 0.141 r_chiral_restr 0.077 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 10892 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 124
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling