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Structural and functional analysis of a loading acyltransferase from the avermectin modular polyketide synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HG4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.75 293 3.4 M sodium formate, pH 6.75, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.82 32.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.21 α = 90 b = 74.29 β = 90 c = 82.42 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 110 CCD MARMOSAIC 225 mm CCD 2014-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97891 SSRF BL17U
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 2 50 99.4 0.073 14.3 4.3 20229 20108 2 2 19.5
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 2 2.11 99.9 0.209 8.1 4.9 2902
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2HG4 2 50 19191 19000 1022 99.01 0.20968 0.20788 0.2176 0.24155 0.2578 RANDOM 25.141
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] -2.9 -1.46 4.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.022 r_dihedral_angle_4_deg 19.165 r_dihedral_angle_3_deg 13.389 r_long_range_B_refined 6.663 r_long_range_B_other 6.663 r_dihedral_angle_1_deg 4.958 r_scangle_other 4.583 r_scbond_it 3.134 r_scbond_other 3.133 r_mcangle_it 2.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.022 r_dihedral_angle_4_deg 19.165 r_dihedral_angle_3_deg 13.389 r_long_range_B_refined 6.663 r_long_range_B_other 6.663 r_dihedral_angle_1_deg 4.958 r_scangle_other 4.583 r_scbond_it 3.134 r_scbond_other 3.133 r_mcangle_it 2.912 r_mcangle_other 2.911 r_mcbond_it 1.979 r_mcbond_other 1.962 r_angle_refined_deg 1.391 r_angle_other_deg 0.703 r_chiral_restr 0.076 r_gen_planes_refined 0.013 r_bond_refined_d 0.01 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2392 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction PHASER phasing REFMAC refinement SCALA data scaling