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Crystal structure of human phosphodiesterase 4b with regulatory domain and d155988
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 100MM NAACETATE, 20MM CALCIUM CHLORIDE, 15% MPD, PH 4.6, VAPOR DIFFUSION, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.52 51.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.004 α = 90 b = 95.004 β = 90 c = 93.714 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2006-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 ALS 5.0.2
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 2.35 50 98.3 0.239 4.5 3.1 38397
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) 2.35 2.41 86.5 0.812 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.63 50 28027 1413 0.181 0.179 0.1849 0.233 0.2347 RANDOM 30.11
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] -0.37 -0.18 -0.37 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.244 r_dihedral_angle_4_deg 19.091 r_dihedral_angle_3_deg 17.918 r_dihedral_angle_1_deg 5.737 r_scangle_it 3.159 r_scbond_it 1.852 r_angle_refined_deg 1.338 r_mcangle_it 1.126 r_angle_other_deg 1.03 r_mcbond_it 0.552
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.244 r_dihedral_angle_4_deg 19.091 r_dihedral_angle_3_deg 17.918 r_dihedral_angle_1_deg 5.737 r_scangle_it 3.159 r_scbond_it 1.852 r_angle_refined_deg 1.338 r_mcangle_it 1.126 r_angle_other_deg 1.03 r_mcbond_it 0.552 r_chiral_restr 0.098 r_mcbond_other 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 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 5977 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 56
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling