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Crystal structure of Bifidobacterium bifidum beta-galactosidase in complex with alpha-galactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UZS PDB ENTRY 4UZS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 292 20% (W/V) POLYETHYLENE GLYCOL 3, 350, 0.2 M DIBASIC AMMONIUM TARTRATE AND 4% (W/V) 1-PROPANOL AT 292 K, pH 6
Crystal Properties Matthews coefficient Solvent content 2.35 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.72 α = 90 b = 101.592 β = 105.4 c = 114.625 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 IMAGE PLATE MARRESEARCH MIRRORS 2010-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 1.9 42.8 97 0.1 13.4 3.7 153059 2
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 1.9 2 85 0.66 2 3.4
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 PDB ENTRY 4UZS 1.94 110.51 145369 7688 97.01 0.15762 0.15505 0.20606 0.1823 RANDOM 25.194
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] 2.35 1.06 -1.98 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.179 r_dihedral_angle_4_deg 16.933 r_dihedral_angle_3_deg 13.759 r_dihedral_angle_1_deg 6.58 r_mcangle_it 2.577 r_scbond_it 2.5 r_mcbond_it 1.843 r_mcbond_other 1.837 r_angle_refined_deg 1.739 r_angle_other_deg 0.909
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.179 r_dihedral_angle_4_deg 16.933 r_dihedral_angle_3_deg 13.759 r_dihedral_angle_1_deg 6.58 r_mcangle_it 2.577 r_scbond_it 2.5 r_mcbond_it 1.843 r_mcbond_other 1.837 r_angle_refined_deg 1.739 r_angle_other_deg 0.909 r_chiral_restr 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16138 Nucleic Acid Atoms Solvent Atoms 2021 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing