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GltA N83K mutant 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 2.03 39.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.995 α = 107.05 b = 42.39 β = 102.06 c = 59.605 γ = 104.29
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 1.56 54.29 86.5 0.076 0.108 0.076 0.94 10.1 1.6 42429 12.63
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 1.56 1.59 0.169 0.239 0.169 0.92 2.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2Z8F 1.56 38.29 40257 2170 86.54 0.1519 0.1498 0.1879 0.2004 RANDOM 20.885
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] 0.63 1.07 1.27 -1.05 -0.12 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.372 r_dihedral_angle_3_deg 12.543 r_dihedral_angle_1_deg 6.194 r_dihedral_angle_4_deg 5.067 r_angle_refined_deg 1.623 r_angle_other_deg 1.51 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.372 r_dihedral_angle_3_deg 12.543 r_dihedral_angle_1_deg 6.194 r_dihedral_angle_4_deg 5.067 r_angle_refined_deg 1.623 r_angle_other_deg 1.51 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2992 Nucleic Acid Atoms Solvent Atoms 397 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing