☰ Navigation Tabs
Crystal Structure of Prophenoloxidase PPO6 chimeric mutant (F215EASNRAIVD224 to G215DGPDSVVR223) from Aedes aegypti
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YZW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291.15 0.1 M imidazole pH7.0, 2% v/v Tacsimate pH7.0, 5% v/v 2-ProOH, 6%-10% v/v PEG 3350,
Crystal Properties Matthews coefficient Solvent content 2.47 50.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.57 α = 90 b = 153.66 β = 90 c = 223.17 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M 2022-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.65 47.69 98.6 0.16 0.173 0.066 12.2 12.6 90756 46.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.7 86.3 0.79 0.907 0.436 2.1 7.9
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 2.65 47.69 86146 4599 98.47 0.18018 0.17585 0.1827 0.26133 0.264 RANDOM 45.045
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] -1.45 -2.16 3.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.12 r_long_range_B_refined 9.55 r_long_range_B_other 9.549 r_dihedral_angle_2_deg 8.128 r_dihedral_angle_1_deg 7.072 r_scangle_other 6.712 r_mcangle_it 5.996 r_mcangle_other 5.996 r_scbond_it 5.844 r_scbond_other 5.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.12 r_long_range_B_refined 9.55 r_long_range_B_other 9.549 r_dihedral_angle_2_deg 8.128 r_dihedral_angle_1_deg 7.072 r_scangle_other 6.712 r_mcangle_it 5.996 r_mcangle_other 5.996 r_scbond_it 5.844 r_scbond_other 5.843 r_mcbond_it 3.825 r_mcbond_other 3.817 r_angle_refined_deg 1.415 r_angle_other_deg 0.466 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 21657 Nucleic Acid Atoms Solvent Atoms 774 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MR-Rosetta phasing