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The crystal Structure PDE delta in complex with R-p9
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 5 277 8% v/v Tacsimate, 20% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.98 58.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.55 α = 90 b = 55.55 β = 90 c = 115.34 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 2016-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97941 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 2.5 50 99.4 0.072 0.028 23.75 8.2 7571
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 99.7 0.35 0.13 7.81 8.2
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 2.5 48.11 7081 398 98.56 0.19829 0.19546 0.2103 0.24528 0.2485 RANDOM 65.725
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] -0.05 -0.02 -0.05 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.183 r_dihedral_angle_4_deg 28.429 r_dihedral_angle_3_deg 14.129 r_long_range_B_other 11.885 r_long_range_B_refined 11.869 r_scangle_other 9.44 r_dihedral_angle_1_deg 7.626 r_mcangle_it 6.667 r_mcangle_other 6.665 r_scbond_it 6.627
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.183 r_dihedral_angle_4_deg 28.429 r_dihedral_angle_3_deg 14.129 r_long_range_B_other 11.885 r_long_range_B_refined 11.869 r_scangle_other 9.44 r_dihedral_angle_1_deg 7.626 r_mcangle_it 6.667 r_mcangle_other 6.665 r_scbond_it 6.627 r_scbond_other 6.623 r_mcbond_it 5.225 r_mcbond_other 5.218 r_angle_refined_deg 1.715 r_angle_other_deg 0.866 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 1209 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling