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Crystal Structure of Prophenoloxidase PPO6 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 6.5 291.15 0.2 M MgCl2,0.1 M Sodium Cacodylate pH6.5,10%-15% v/v PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.54 51.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.041 α = 90 b = 364.149 β = 118.95 c = 125.522 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER X 9M 2022-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X17B1 0.920 NSLS X17B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 3.15 48.66 98.8 0.241 0.241 0.278 0.135 0.967 5 3.8 161746
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.15 3.32 98.8 0.91 0.499 0.429 1.5 3.7
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 3.15 48.66 153764 7921 98.72 0.27134 0.26932 0.2693 0.31041 0.308 RANDOM 66.886
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 0.62 -1.08 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.178 r_long_range_B_refined 12.417 r_long_range_B_other 12.417 r_mcangle_it 8.037 r_mcangle_other 8.037 r_scangle_other 7.183 r_dihedral_angle_1_deg 6.338 r_dihedral_angle_2_deg 4.826 r_mcbond_it 4.778 r_mcbond_other 4.778
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.178 r_long_range_B_refined 12.417 r_long_range_B_other 12.417 r_mcangle_it 8.037 r_mcangle_other 8.037 r_scangle_other 7.183 r_dihedral_angle_1_deg 6.338 r_dihedral_angle_2_deg 4.826 r_mcbond_it 4.778 r_mcbond_other 4.778 r_scbond_it 4.177 r_scbond_other 4.177 r_angle_refined_deg 1.286 r_angle_other_deg 0.495 r_chiral_restr 0.064 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 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 64944 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MR-Rosetta phasing