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Ketosynthase (ApeO) in Complex with its Chain Length Factor (ApeC) from Xenorhabdus doucetiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IWZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 1 M Sodium/Potassium Phosphate
Crystal Properties Matthews coefficient Solvent content 2.16 43.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.95 α = 90 b = 88.89 β = 108.13 c = 63 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 16M 2018-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.45 30 98.3 0.043 12.9 3.5 103673
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.55 96.9 0.657 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 2IWZ 1.45 30 98482 5183 98.37 0.13031 0.12861 0.1294 0.16247 0.1669 RANDOM 25.292
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] 0.76 0.43 0.21 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.721 r_sphericity_free 28.845 r_dihedral_angle_4_deg 19.479 r_sphericity_bonded 14.111 r_dihedral_angle_3_deg 12.897 r_dihedral_angle_1_deg 6.416 r_long_range_B_refined 3.764 r_long_range_B_other 3.585 r_scangle_other 3.219 r_scbond_it 2.672
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.721 r_sphericity_free 28.845 r_dihedral_angle_4_deg 19.479 r_sphericity_bonded 14.111 r_dihedral_angle_3_deg 12.897 r_dihedral_angle_1_deg 6.416 r_long_range_B_refined 3.764 r_long_range_B_other 3.585 r_scangle_other 3.219 r_scbond_it 2.672 r_scbond_other 2.672 r_mcangle_it 2.417 r_mcangle_other 2.417 r_mcbond_it 1.875 r_mcbond_other 1.869 r_angle_other_deg 1.394 r_rigid_bond_restr 1.345 r_angle_refined_deg 1.338 r_chiral_restr 0.071 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4842 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing