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Crystal structure of a gh29 alpha-l-fucosidase gh29 from bacteroides thetaiotaomicron in a novel crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WVV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291.15 17% PEG 6K, 0.124M ammonium sulfate, 0.1M imidazole 2 parts protein: 3 mother liquor, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Crystal Properties Matthews coefficient Solvent content 3.07 59.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.15 α = 90 b = 96.55 β = 91.3 c = 97.27 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 CCD MAR CCD 165 mm 2011-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.59 30.666 100 0.112 8.2 3.8 164706 164706
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.68 99.9 0.878 0.878 0.9 3.7 23967
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 2WVV 1.59 30.666 159881 8454 99.94 0.1587 0.1577 0.1775 0.183 RANDOM 15.8145
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] 1.12 -0.29 0.03 -1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.036 r_dihedral_angle_4_deg 20.764 r_dihedral_angle_3_deg 11.888 r_dihedral_angle_1_deg 5.805 r_mcangle_it 1.719 r_angle_refined_deg 1.477 r_mcbond_it 1.101 r_mcbond_other 1.1 r_angle_other_deg 1.056 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.036 r_dihedral_angle_4_deg 20.764 r_dihedral_angle_3_deg 11.888 r_dihedral_angle_1_deg 5.805 r_mcangle_it 1.719 r_angle_refined_deg 1.477 r_mcbond_it 1.101 r_mcbond_other 1.1 r_angle_other_deg 1.056 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7075 Nucleic Acid Atoms Solvent Atoms 1059 Heterogen Atoms 69
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction