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The crystal Structure PDE delta in complex with compound (R, R)-1g
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JV6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 277 0.1 M Sodium acetate, 30 %(v/v) PEG 300
Crystal Properties Matthews coefficient Solvent content 2.96 58.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.7 α = 90 b = 55.7 β = 90 c = 114.902 γ = 120
Symmetry Space Group P 32 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 AREA DETECTOR ADSC QUANTUM 315r 2016-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97913 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.25 50 99.9 0.112 0.04 24.4 9.2 10393
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.29 100 0.208 11.93 9.4
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 4JV6 2.25 36.94 9805 557 99.91 0.1842 0.181 0.1899 0.24119 0.2392 RANDOM 40.307
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.746 r_dihedral_angle_4_deg 19.043 r_dihedral_angle_3_deg 13.799 r_long_range_B_refined 8.803 r_long_range_B_other 8.8 r_scangle_other 7.101 r_dihedral_angle_1_deg 6.813 r_scbond_it 4.723 r_scbond_other 4.722 r_mcangle_it 4.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.746 r_dihedral_angle_4_deg 19.043 r_dihedral_angle_3_deg 13.799 r_long_range_B_refined 8.803 r_long_range_B_other 8.8 r_scangle_other 7.101 r_dihedral_angle_1_deg 6.813 r_scbond_it 4.723 r_scbond_other 4.722 r_mcangle_it 4.316 r_mcangle_other 4.313 r_mcbond_other 3.316 r_mcbond_it 3.315 r_angle_refined_deg 1.838 r_angle_other_deg 1.025 r_chiral_restr 0.106 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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 1222 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling