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Adenylation domain structure from NRPS-like Delta-Poly-L-Ornithine synthetase (L-Lysine bound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8G95 Apo structure 8G95 was used as search model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7 293.15 0.1 M Amm Bromide, 0.1 M BTP pH 7.0, 24% PEG 20K
Crystal Properties Matthews coefficient Solvent content 2.5 50.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.48 α = 90 b = 91.978 β = 90 c = 152.246 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 PIXEL DECTRIS PILATUS3 6M 2019-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03322 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.49 58.64 99.53 0.1269 0.0368 0.999 15.54 12.8 31880 62.24
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 2.49 2.57 0.5
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 8G95 2.49 58.64 1.34 31869 1999 99.53 0.1984 0.195 0.1976 0.2487 0.2514 78.37
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 11.2728 f_angle_d 0.9655 f_chiral_restr 0.0555 f_bond_d 0.0079 f_plane_restr 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6104 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 82
Software Software Software Name Purpose PHENIX refinement Coot model building AutoProcess data reduction PHASER phasing autoPROC data reduction Aimless data scaling