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Crystal structure of LamA_E269S from Z. galactanivorans in complex with laminaritriose and laminaritetraose
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 4 293 100 MM MIB PH 4.0, 19% PEG1500, HANGING DROP AT 20 DEGREES CELSIUS MIXING 2 MICROL OF PROTEIN (13.7 MG/ML SUPPLEMENTED WITH 5 MM PURIFIED LAMINARIHEXAOSE) WITH 1 MICROL OF RESERVOIR SOLUTION
Crystal Properties Matthews coefficient Solvent content 2.08 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.459 α = 90 b = 76.495 β = 90 c = 142.941 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 1.35 40.44 99.7 0.04 16.3 4.7 107451
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 1.35 1.42 99.7 0.55 2.3 4.7
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 PDB ENTRY 4BQ1 1.35 67.44 102000 5366 99.55 0.13184 0.13 0.1356 0.16666 0.1739 RANDOM 23.543
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] 1.14 -0.29 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.157 r_dihedral_angle_4_deg 29.917 r_sphericity_free 28.182 r_sphericity_bonded 16.704 r_dihedral_angle_3_deg 12.438 r_rigid_bond_restr 8.582 r_dihedral_angle_1_deg 7.795 r_angle_refined_deg 2.324 r_chiral_restr 0.257 r_bond_refined_d 0.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.157 r_dihedral_angle_4_deg 29.917 r_sphericity_free 28.182 r_sphericity_bonded 16.704 r_dihedral_angle_3_deg 12.438 r_rigid_bond_restr 8.582 r_dihedral_angle_1_deg 7.795 r_angle_refined_deg 2.324 r_chiral_restr 0.257 r_bond_refined_d 0.026 r_gen_planes_refined 0.015 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 4004 Nucleic Acid Atoms Solvent Atoms 545 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing