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PDE4B bound to MAPI compound 92a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 50 mM CALCIUM ACETATE, 20% PEG 400,
100 mM SODIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 2.34 47.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.76 α = 90 b = 95.76 β = 90 c = 85.46 γ = 120
Symmetry Space Group P 31 2 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 PIXEL DECTRIS PILATUS 6M 2015-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.89 85.46 99.5 0.997 13.8 8.4 36474
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.94 0.497
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 1.89 83.07 34670 1771 99.48 0.1595 0.15774 0.191 0.19509 0.2274 RANDOM 22.371
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] -0.16 -0.08 -0.16 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.2 r_dihedral_angle_4_deg 20.268 r_dihedral_angle_3_deg 16.623 r_dihedral_angle_1_deg 6.785 r_long_range_B_refined 5.7 r_long_range_B_other 5.7 r_scangle_other 4.977 r_scbond_it 3.235 r_scbond_other 3.234 r_mcangle_it 2.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.2 r_dihedral_angle_4_deg 20.268 r_dihedral_angle_3_deg 16.623 r_dihedral_angle_1_deg 6.785 r_long_range_B_refined 5.7 r_long_range_B_other 5.7 r_scangle_other 4.977 r_scbond_it 3.235 r_scbond_other 3.234 r_mcangle_it 2.52 r_mcangle_other 2.52 r_angle_refined_deg 2.476 r_mcbond_it 1.962 r_mcbond_other 1.842 r_angle_other_deg 1.301 r_chiral_restr 0.172 r_bond_refined_d 0.029 r_gen_planes_refined 0.014 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2714 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 51
Software Software Software Name Purpose Aimless data scaling autoPROC data processing xia2 data reduction XDS data reduction pointless data scaling PHASER phasing REFMAC refinement