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Crystal Structure of GH136 lacto-N-biosidase from Eubacterium ramulus - selenomethionine derivative
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 20% PEG 6000, 0.1 M Tris-HCl (pH 8.5), 1 M LiCl
Crystal Properties Matthews coefficient Solvent content 2.75 55.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.734 α = 90 b = 132.734 β = 90 c = 82.466 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 DECTRIS PILATUS 2M-F 2018-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.978 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.4 45.75 100 0.145 0.999 12.2 20.1 155798
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 100 1.909 0.728 1.7 19.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.4 45.75 155798 8043 99.97 0.1498 0.1487 0.1515 0.1724 0.1744 RANDOM 19.614
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.855 r_dihedral_angle_4_deg 16.005 r_dihedral_angle_3_deg 11.255 r_dihedral_angle_1_deg 7.35 r_angle_refined_deg 1.975 r_angle_other_deg 1.591 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.855 r_dihedral_angle_4_deg 16.005 r_dihedral_angle_3_deg 11.255 r_dihedral_angle_1_deg 7.35 r_angle_refined_deg 1.975 r_angle_other_deg 1.591 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5028 Nucleic Acid Atoms Solvent Atoms 835 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHENIX phasing