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Adenylation domain structure from NRPS-like Delta-Poly-L-Ornithine synthetase (L-Ornithine bound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8G95
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 = 63.975 α = 90 b = 92.785 β = 90 c = 152.644 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 2.3 79.29 95.41 0.1403 0.04061 0.999 13.35 12.8 39481 55.54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.37 0.9639 0.416
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 2.3 79.29 1.33 39451 1998 95.4 0.2077 0.2061 0.21 0.2377 0.2396 76.12
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 11.6919 f_angle_d 0.7889 f_chiral_restr 0.0482 f_plane_restr 0.0051 f_bond_d 0.0036
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6336 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement Coot model building AutoProcess data reduction PHASER phasing autoPROC data reduction Aimless data scaling