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Klebsiella oxytoca NpsA N-terminal subdomain in space group C2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VSQ
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 2.06 40.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.597 α = 90 b = 60.088 β = 103.542 c = 80.775 γ = 90
Symmetry Space Group C 1 2 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 PILATUS3 6M 2019-03-25 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 1.84 46.76 96.3 0.083 0.09 0.034 0.999 10.2 6.8 29872 36.28
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 1.84 1.87 96.9 2.103 2.286 0.886 0.335 0.9 6.5
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 2vsq 1.84 46.76 1.34 29864 1553 96.23 0.21 0.2078 0.2084 0.2483 0.2475 52.98
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 12.5188 f_angle_d 1.2102 f_chiral_restr 0.0703 f_bond_d 0.0117 f_plane_restr 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2757 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 3
Software Software Software Name Purpose XDS data reduction Aimless data scaling autoPROC data scaling PHASER phasing Coot model building PHENIX refinement