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Klebsiella oxytoca NpsA N-terminal subdomain in complex with anthranilyl-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 VAPOR DIFFUSION, HANGING DROP 293 well solution: 100 mM HEPES pH 7.5, 150 mM KBr, 30% w/v PEG3350
protein solution (15 mg/mL): 50 mM HEPES pH 8.0, 150 mM NaCl, 0.2 mM TCEP
hanging drops: 1 uL protein solution, 1 uL well solution
Crystal Properties Matthews coefficient Solvent content 2.13 42.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.013 α = 90 b = 61.408 β = 100.434 c = 80.518 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 PILATUS 6M 2019-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
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 2.12 79.19 92.1 0.055 0.06 0.023 0.999 17.5 6.7 38904 45.91
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 2.12 2.16 97.6 0.792 0.861 0.332 0.852 2.2 6.6
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 2.12 50.37 1.34 38876 1853 92.04 0.2039 0.2027 0.208 0.2273 0.2334 59.79
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 16.0061 f_angle_d 0.8113 f_chiral_restr 0.0599 f_bond_d 0.0069 f_plane_restr 0.0044
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5632 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 62
Software Software Software Name Purpose XDS data reduction Aimless data scaling autoPROC data scaling PHASER phasing Coot model building PHENIX refinement