☰ Navigation Tabs
Adenylation domain structure from NRPS-like Delta-Poly-L-Ornithine synthetase (D-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 = 63.837 α = 90 b = 93.928 β = 90 c = 152.257 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 PILATUS 6M 2019-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
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 2.51 93.93 98.26 0.0924 0.03841 0.999 15.04 6.7 31440 59.6
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 2.51 2.65 0.506
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 2.51 48.92 1.34 31374 1994 98.29 0.1972 0.1944 0.2033 0.2396 0.2408 74.62
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 12.3538 f_angle_d 0.6003 f_chiral_restr 0.0452 f_plane_restr 0.0042 f_bond_d 0.0029
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6234 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 61
Software Software Software Name Purpose PHENIX refinement Coot model building AutoProcess data reduction PHASER phasing autoPROC data reduction Aimless data scaling