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Wild type GltA from Bifidobacterium infantis JCM 1222 complexed with lacto-N-tetraose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z8F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293.15 30% (w/v) PEG MME 550, 10mM ZnSO4, 0.1M MES-NaOH (pH 5.5)
Crystal Properties Matthews coefficient Solvent content 1.99 38.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.138 α = 97.41 b = 84.381 β = 92.25 c = 106.688 γ = 89.92
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 EIGER X 16M 2016-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
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 1.55 47.59 95.5 0.075 0.106 0.075 0.97 5.8 1.8 187561 4.9
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 1.55 1.58 85.7 0.355 0.502 0.311 0.725 2 1.7
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 2Z8F 1.55 47.59 178122 9435 95.53 0.1927 0.1909 0.2006 0.2271 0.2339 RANDOM 10.99
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] -0.07 0.06 -0.03 -0.63 -0.15 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.504 r_dihedral_angle_3_deg 13.458 r_dihedral_angle_1_deg 6.302 r_dihedral_angle_4_deg 5.154 r_angle_refined_deg 1.694 r_angle_other_deg 1.54 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.504 r_dihedral_angle_3_deg 13.458 r_dihedral_angle_1_deg 6.302 r_dihedral_angle_4_deg 5.154 r_angle_refined_deg 1.694 r_angle_other_deg 1.54 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11940 Nucleic Acid Atoms Solvent Atoms 1525 Heterogen Atoms 217
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing