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Crystal structure of a galactokinase from Bifidobacterium infantis in complex with Galactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TEP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M MES pH 6.0, 0.15 - 0.25 M NaCl and 18 - 22 % (w/v) polyethylene glycol 6000)
Crystal Properties Matthews coefficient Solvent content 2.67 53.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.32 α = 90 b = 164.929 β = 94.97 c = 113.63 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 2018-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.68 82.6 94.7 0.108 4.9 3.2 205822
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.71 0.553
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 6TEP 1.68 82.6 195339 10249 94.55 0.2278 0.2236 0.2309 0.308 0.3119 RANDOM 24.385
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] -1.51 -1.88 -1.07 2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.91 r_dihedral_angle_3_deg 16.146 r_dihedral_angle_4_deg 15.927 r_dihedral_angle_1_deg 7.577 r_rigid_bond_restr 5.843 r_angle_refined_deg 1.853 r_angle_other_deg 1.402 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.91 r_dihedral_angle_3_deg 16.146 r_dihedral_angle_4_deg 15.927 r_dihedral_angle_1_deg 7.577 r_rigid_bond_restr 5.843 r_angle_refined_deg 1.853 r_angle_other_deg 1.402 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12381 Nucleic Acid Atoms Solvent Atoms 764 Heterogen Atoms 520
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling MOLREP phasing