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Human PDE-papaverine complex obtained by ligand soaking of cross- linked protein crystals
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OUP PDB ENTRY 2OUP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.25 16% PEG3350, 60 MM BETA-MERCAPTOETHANOL,0.1 M HEPES PH 7.25,0.2 M MGCL2
Crystal Properties Matthews coefficient Solvent content 2.06 40.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.84 α = 90 b = 81.57 β = 90 c = 157.55 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 IMAGE PLATE VARIMAX MIRRORS 2008-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
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 2.8 56.7 100 0.136 13.3 6.5 15959 6 72.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 99.9 0.69 0.694 2.2 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 2OUP 2.8 56.7 15959 843 100 0.242 0.239 0.2326 0.3 0.2946 RANDOM 67.06
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] 9.84 -6.33 -3.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.272 r_dihedral_angle_3_deg 16.765 r_dihedral_angle_4_deg 16.012 r_dihedral_angle_1_deg 4.748 r_angle_refined_deg 1.049 r_scangle_it 1.032 r_mcangle_it 0.86 r_scbond_it 0.633 r_mcbond_it 0.471 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.272 r_dihedral_angle_3_deg 16.765 r_dihedral_angle_4_deg 16.012 r_dihedral_angle_1_deg 4.748 r_angle_refined_deg 1.049 r_scangle_it 1.032 r_mcangle_it 0.86 r_scbond_it 0.633 r_mcbond_it 0.471 r_nbtor_refined 0.299 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.195 r_xyhbond_nbd_refined 0.138 r_symmetry_hbond_refined 0.114 r_metal_ion_refined 0.096 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5258 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling MOLREP phasing