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Crystal structure of lamA_E269S from Zobellia galactanivorans in complex with a trisaccharide of 1,3-1,4-beta-D-glucan.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BQ1 PDB ENTRY 4BQ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 285 MONO-CRYSTALS OF LAMAE269S IN COMPLEX WITH MLG TRISACCHARIDES WERE OBTAINED AS FOLLOWED: 2 MICROL OF THE MIXTURE ENZYME/OLIGOSACCHARIDES (11,7 MG.ML-1 OF ENZYME, 0,04% (W/V) OF MLG DEGRADATION PRODUCTS) WERE ADDED TO 1 MICROL OF RESERVOIR SOLUTION CONTAINING 100 MM MIB BUFFER PH4.0, 17% OF PEG 1500 AND 10% OF GLYCEROL IN HANGING DROPS AT 12 CELSIUS DEGREE
Crystal Properties Matthews coefficient Solvent content 2.08 40.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.528 α = 90 b = 76.485 β = 90 c = 142.674 γ = 90
Symmetry Space Group P 21 21 21
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 6M 2011-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.13 47.56 99.2 0.07 10.5 4.9 181382
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 1.13 1.19 95.7 0.66 1.9 4.2
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 PDB ENTRY 4BQ1 1.13 71.34 172173 9107 99.06 0.14404 0.14241 0.1448 0.17452 0.1759 RANDOM 20.351
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] 0.86 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.659 r_dihedral_angle_4_deg 27.662 r_sphericity_free 27.462 r_sphericity_bonded 13.422 r_dihedral_angle_3_deg 12.29 r_rigid_bond_restr 8.494 r_dihedral_angle_1_deg 7.678 r_angle_refined_deg 2.3 r_chiral_restr 0.235 r_bond_refined_d 0.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.659 r_dihedral_angle_4_deg 27.662 r_sphericity_free 27.462 r_sphericity_bonded 13.422 r_dihedral_angle_3_deg 12.29 r_rigid_bond_restr 8.494 r_dihedral_angle_1_deg 7.678 r_angle_refined_deg 2.3 r_chiral_restr 0.235 r_bond_refined_d 0.026 r_gen_planes_refined 0.016 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4054 Nucleic Acid Atoms Solvent Atoms 584 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing