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Crystal structure of PDE3B in complex with GSK4394835A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SOJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.2 M NaCl, 25%PEG3350,0.1 M bis-Tris pH6.5, cryo: 25% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.61 52.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.586 α = 90 b = 78.586 β = 90 c = 166.339 γ = 90
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 2M 2021-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9655 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.68 71.16 92.7 0.34 0.986 6.8 4.8 18157
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.68 3.022 66.6 1.648 0.511 8.6
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 2.7 71.16 17311 841 65.67 0.17888 0.17674 0.1803 0.22352 0.2237 RANDOM 49.957
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] 0.14 0.14 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.754 r_dihedral_angle_4_deg 19.046 r_dihedral_angle_3_deg 14.972 r_long_range_B_refined 8.611 r_long_range_B_other 8.61 r_dihedral_angle_1_deg 6.446 r_scangle_other 5.785 r_mcangle_it 5.416 r_mcangle_other 5.415 r_scbond_it 3.532
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.754 r_dihedral_angle_4_deg 19.046 r_dihedral_angle_3_deg 14.972 r_long_range_B_refined 8.611 r_long_range_B_other 8.61 r_dihedral_angle_1_deg 6.446 r_scangle_other 5.785 r_mcangle_it 5.416 r_mcangle_other 5.415 r_scbond_it 3.532 r_scbond_other 3.531 r_mcbond_other 3.374 r_mcbond_it 3.373 r_angle_refined_deg 1.336 r_angle_other_deg 1.237 r_chiral_restr 0.055 r_bond_refined_d 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5716 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing