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KS-AT didomain from module 2 of the 6-deoxyerythronolide B synthase in complex with antibody fragment AA5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C9U PDB entry 6C9U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 Morpheus reagents (0.1 M Carboxylic Acids Mix, 0.1 M Buffer System 2, pH 7.0, 30.6 % v/v Precipitant Mix 2), Silver bullet reagents (0.004 M cadmium chloride hydrate, 0.004 M cobalt(II) chloride hexahydrate, 0.004 M copper(II) chloride dihydrate, 0.004 nickel(II) chloride hexahydrate, 0.02 M HEPES sodium, pH 6.8)
Crystal Properties Matthews coefficient Solvent content 3.48 64.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 249.37 α = 90 b = 252.44 β = 90 c = 63.92 γ = 90
Symmetry Space Group P 21 21 2
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 PILATUS 6M 2022-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.7 39.62 98.3 0.162 0.165 0.999 17.97 27.077 110267 73.62
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.77 98.7 2.991 3.049 0.599 1.66 26.322
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 6C9U 2.7 39.62 1.34 110217 5510 98.32 0.2262 0.2248 0.2245 0.2538 0.2535 80.56
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.0862 f_angle_d 1.2647 f_chiral_restr 0.0716 f_plane_restr 0.025 f_bond_d 0.0105
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17684 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing