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The crystal Structure PDE delta in complex with (rac)-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 277 0.2 M Ammonium citrate dibasic, 20% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.95 58.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.568 α = 90 b = 55.568 β = 90 c = 115.465 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 2015-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97915 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 1.95 50 99.7 0.066 0.019 38.61 13.9 15663
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 1.95 1.98 100 0.481 0.132 7.4 14.2
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 1.95 48.12 14524 742 97.37 0.18968 0.18748 0.1974 0.23142 0.2347 RANDOM 27.645
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] -0.12 -0.06 -0.12 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.947 r_dihedral_angle_4_deg 14.844 r_dihedral_angle_3_deg 13.523 r_dihedral_angle_1_deg 7.572 r_long_range_B_refined 6.072 r_long_range_B_other 6.07 r_scangle_other 3.481 r_scbond_it 2.184 r_scbond_other 2.182 r_mcangle_it 2.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.947 r_dihedral_angle_4_deg 14.844 r_dihedral_angle_3_deg 13.523 r_dihedral_angle_1_deg 7.572 r_long_range_B_refined 6.072 r_long_range_B_other 6.07 r_scangle_other 3.481 r_scbond_it 2.184 r_scbond_other 2.182 r_mcangle_it 2.168 r_mcangle_other 2.166 r_angle_refined_deg 2.089 r_mcbond_other 1.373 r_mcbond_it 1.372 r_angle_other_deg 0.971 r_chiral_restr 0.131 r_bond_refined_d 0.023 r_gen_planes_refined 0.013 r_bond_other_d 0.002 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 1212 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling