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HalA with lysine, succinate, chloride, and vanadium(IV)-oxo at pH 4.2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JSD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 HalA crystals were obtained by the sitting drop vapor diffusion method by combining equal volumes of protein solution (HalA (15 mg/ml), lysine (50 mM, pH 7), sodium succinate (20 mM, pH 7), sodium chloride (100 mM) and vanadium(IV) oxide sulfate hydrate (1 mM, dissolved in 2.5 mM H2SO4)) and reservoir solution (sodium phosphate dibasic/citric acid (100 mM), 40% (w/v) PEG 300, pH 4.2)
Crystal Properties Matthews coefficient Solvent content 2.51 50.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.95 α = 90 b = 146.95 β = 90 c = 287.97 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 PIXEL DECTRIS PILATUS3 S 6M 2021-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11583 ALS 8.3.1
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 1.93 95.99 99.6 0.361 0.368 0.07 0.999 13.5 53.12 173594
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 1.93 1.96 94.3 5.306 5.528 1.517 0.536 0.7 24.77
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 1.93 95.35 1.96 173238 8718 99.37 0.1766 0.1745 0.1749 0.2163 0.2163
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 14.891 f_angle_d 0.813 f_chiral_restr 0.05 f_plane_restr 0.009 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15845 Nucleic Acid Atoms Solvent Atoms 1418 Heterogen Atoms 237
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing