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Crystal structure of HCAN_0198, a 3,4-ketoisomerase from Helicobacter canadensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TPU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 protein incubated with 5 mM TDP. precipitant = 7-13% PEG-8000, 1 M tetramethyl ammonium chloride, 100 mM HEPES (pH 7.5)
Crystal Properties Matthews coefficient Solvent content 2.93 57.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.944 α = 90 b = 92.944 β = 90 c = 85.55 γ = 120
Symmetry Space Group P 31 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 Bruker PHOTON II 2021-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.5 50 98.5 0.048 20.3 16.1 14924
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 98.7 0.346 3.6 9.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5tpu 2.5 24.79 14191 733 98.48 0.2044 0.2004 0.2047 0.2776 0.2751 RANDOM 35.853
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] -0.09 -0.04 -0.09 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.602 r_dihedral_angle_4_deg 27.026 r_dihedral_angle_3_deg 18.38 r_dihedral_angle_1_deg 7.566 r_angle_refined_deg 1.465 r_angle_other_deg 1.189 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.602 r_dihedral_angle_4_deg 27.026 r_dihedral_angle_3_deg 18.38 r_dihedral_angle_1_deg 7.566 r_angle_refined_deg 1.465 r_angle_other_deg 1.189 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2205 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction SADABS data scaling PHASER phasing