☰ Navigation Tabs
Crystal structure of human phosphodiesterase 4d with rolipram
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 100MM HEPES PH 7.5, 35% ETHYLENE GLYCOL, 5% GLYCEROL, 22% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.54 51.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.611 α = 90 b = 112.758 β = 90 c = 160.034 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 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97 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 1.95 50 99.6 0.066 11.5 131239
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) 1.95 1.98 100 0.699
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 1.95 50 129779 6540 0.185 0.183 0.1879 0.215 0.2181 RANDOM 23.61
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] 0.69 -0.47 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.569 r_dihedral_angle_4_deg 17.66 r_dihedral_angle_3_deg 13.921 r_dihedral_angle_1_deg 4.845 r_scangle_it 2.658 r_scbond_it 1.809 r_angle_refined_deg 1.173 r_mcangle_it 1.077 r_angle_other_deg 0.899 r_mcbond_it 0.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.569 r_dihedral_angle_4_deg 17.66 r_dihedral_angle_3_deg 13.921 r_dihedral_angle_1_deg 4.845 r_scangle_it 2.658 r_scbond_it 1.809 r_angle_refined_deg 1.173 r_mcangle_it 1.077 r_angle_other_deg 0.899 r_mcbond_it 0.746 r_symmetry_vdw_other 0.249 r_symmetry_vdw_refined 0.227 r_mcbond_other 0.222 r_nbd_refined 0.214 r_nbd_other 0.184 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.116 r_nbtor_other 0.085 r_chiral_restr 0.064 r_metal_ion_refined 0.052 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other 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 10624 Nucleic Acid Atoms Solvent Atoms 1034 Heterogen Atoms 199
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling