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Crystal structure of human phosphodiesterase 4d with d155988/pmnpq
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 2.57 52.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.385 α = 90 b = 113.57 β = 90 c = 161.129 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 IMAGE PLATE RIGAKU RAXIS MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 2.05 50 90.1 0.058 13.3 5.8 102588
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) 2.05 2.12 53.1 0.436 4.8
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 2.05 49.21 102529 5158 0.173 0.171 0.1739 0.213 0.2149 RANDOM 22.54
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] 0.11 -0.08 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.271 r_dihedral_angle_4_deg 15.274 r_dihedral_angle_3_deg 14.307 r_dihedral_angle_1_deg 5.101 r_scangle_it 3.042 r_scbond_it 1.871 r_angle_refined_deg 1.15 r_mcangle_it 1.134 r_angle_other_deg 0.887 r_mcbond_it 0.584
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.271 r_dihedral_angle_4_deg 15.274 r_dihedral_angle_3_deg 14.307 r_dihedral_angle_1_deg 5.101 r_scangle_it 3.042 r_scbond_it 1.871 r_angle_refined_deg 1.15 r_mcangle_it 1.134 r_angle_other_deg 0.887 r_mcbond_it 0.584 r_mcbond_other 0.131 r_chiral_restr 0.065 r_bond_refined_d 0.011 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 10762 Nucleic Acid Atoms Solvent Atoms 1144 Heterogen Atoms 185
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling