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Crystal Structure of ArnB Transferase from Klebsiella aerogenes (Lattice Translocation Disorder, P21 form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MDO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 Proplex H12: 15% Ethanol, 5% MPD, 0.1M Tris pH 8.5, 0.1 M NaCl, KlaeA.17333.b.B1.PW39179 at 27 mg/mL. Plate: 13222, well H12 drop 2. Puck: PSL-1014, Cryo: CRYO: 50% Crystallant + 50% MPD. 2mM PLP and 2-oxoglutaric acidadded prior to crystallization. Partial occupanyc of PLP-Lys182 adduct and PLP-Tris adduct. The structure factors were corrected for lattice translocation disorder which caused initial high Rfactors (~25%)
Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.084 α = 90 b = 101.351 β = 101.78 c = 68.483 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 9M 2022-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9795 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.55 101.35 99.9 0.12 0.132 0.053 0.998 6.1 5.9 116036
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.59 99.9 0.971 1.072 0.449 0.868 5.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.55 58.82 1.33 115703 5787 99.65 0.1992 0.1981 0.2068 0.2199 0.228
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 12.092 f_angle_d 0.85 f_chiral_restr 0.053 f_plane_restr 0.007 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5624 Nucleic Acid Atoms Solvent Atoms 549 Heterogen Atoms 53
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing