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Crystal structure of a galactokinase from Bifidobacterium infantis in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PIE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING 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 2.7 54.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.272 α = 90 b = 164.495 β = 95.8 c = 115.873 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 PILATUS3 6M 2017-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 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 1.45 94.58 98.4 0.095 7.3 4 336915
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 1.45 1.47 95.6 0.663
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 1PIE 1.45 94.58 319927 16932 98.26 0.1871 0.184 0.1891 0.2449 0.2483 RANDOM 17.661
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] -0.41 -0.95 0.43 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.865 r_dihedral_angle_4_deg 17.29 r_dihedral_angle_3_deg 13.54 r_dihedral_angle_1_deg 6.918 r_rigid_bond_restr 4.836 r_angle_refined_deg 1.939 r_angle_other_deg 1.635 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.865 r_dihedral_angle_4_deg 17.29 r_dihedral_angle_3_deg 13.54 r_dihedral_angle_1_deg 6.918 r_rigid_bond_restr 4.836 r_angle_refined_deg 1.939 r_angle_other_deg 1.635 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12295 Nucleic Acid Atoms Solvent Atoms 1475 Heterogen Atoms 261
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling PHASER phasing