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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 7Q0Q
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 2.4 48.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.957 α = 90 b = 100.489 β = 90 c = 131.908 γ = 90
Symmetry Space Group P 21 2 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 2018-10-23 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) 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 1.43 46.95 98.5 0.999 11.9 3.4 219293 17.45
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 1.43 1.48 0.385
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 7Q0Q 1.43 47.15 1.97 411501 20542 95.3 0.1776 0.1764 0.1717 0.2004 0.1961 25.11
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 12.8589 f_angle_d 1.3328 f_chiral_restr 0.079 f_plane_restr 0.0071 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8151 Nucleic Acid Atoms Solvent Atoms 1143 Heterogen Atoms 414
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement Coot model building