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Acetyltrasferase(3) type IIIa in complex with 3-N-methyl-nemycin B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HT0 5ht0,7kes,6mb9,6np4 experimental model PDB 7KES 5ht0,7kes,6mb9,6np4 experimental model PDB 6MB9 5ht0,7kes,6mb9,6np4 experimental model PDB 6NP4 5ht0,7kes,6mb9,6np4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 7-14% PEG 10,000, 0.1 M Na Acetate, 0.1 M Bis-Tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.53 51.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.59 α = 90 b = 89.235 β = 90 c = 103.248 γ = 90
Symmetry Space Group P 2 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 PIXEL DECTRIS EIGER R 4M 2018-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.987 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.96 19.67 99.13 0.1743 0.996 8.04 7.2 43209 30.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.03 0.551
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5ht0,7kes,6mb9,6np4 1.96 19.87 1.91 81711 4026 98.84 0.1918 0.1896 0.2358 0.1975 34.43
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 9.1807 f_angle_d 1.0385 f_chiral_restr 0.0586 f_bond_d 0.0082 f_plane_restr 0.0078
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4069 Nucleic Acid Atoms Solvent Atoms 493 Heterogen Atoms 69
Software Software Software Name Purpose XDS data reduction PHENIX refinement Aimless data scaling PHASER phasing Coot model building