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Klebsiella oxytoca NpsA in complex with 3-hydroxyanthranilyl-AMSN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VHU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.6 296 well solution: 400 mM imidazole pH 6.6, 10% w/v PEG8000/10000/12000/20000, 2.5% w/v 1,3-dimethylimidazolium dimethyl phosphate
protein solution (16 mg/mL): 10 mM HEPES pH 8.0, 25 mM NaCl, 0.4 mM TCEP, 5 mM 3HA-AMSN
droplet: 2 uL protein solution, 1 uL well solution
Crystal Properties Matthews coefficient Solvent content 2.44 49.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.689 α = 90 b = 87.817 β = 90 c = 165.778 γ = 90
Symmetry Space Group I 2 2 2
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 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 Sym 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 2.89 68.1 99.9 0.149 0.163 0.063 0.997 9.4 6.5 12516 86.74
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.89 2.95 100 2.088 2.261 0.858 0.412 0.9 6.8
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 6vhu 2.89 68.1 1.34 12507 604 99.81 0.2198 0.2176 0.2184 0.262 0.2598 97.58
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 15.5826 f_angle_d 0.5558 f_chiral_restr 0.0467 f_plane_restr 0.0046 f_bond_d 0.0038
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3672 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 33
Software Software Software Name Purpose XDS data reduction Aimless data scaling autoPROC data scaling PHASER phasing Coot model building PHENIX refinement