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Crystal structure of a putative alpha-galactosidase (BF1418) from Bacteroides fragilis NCTC 9343 at 1.57 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.16M magnesium acetate, 20.0% Glycerol, 16.0% polyethylene glycol 8000, 0.1M sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.35 47.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.614 α = 90 b = 114.614 β = 90 c = 77.051 γ = 90
Symmetry Space Group P 42 21 2
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 ADSC QUANTUM 315 KOHZU: Double Crystal Si(111) 2013-10-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.918401,0.979261,0.979152 ALS 8.2.1
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 1.57 29.386 99.1 0.076 9.28 71815 -3 22.74
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 1.57 1.63 94.7 0.947 1.5
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 MAD THROUGHOUT 1.57 29.386 71742 3628 99.75 0.1549 0.1541 0.1639 0.1685 0.1774 RANDOM 27.1649
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] -0.41 -0.41 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.487 r_dihedral_angle_4_deg 12.63 r_dihedral_angle_3_deg 11.527 r_dihedral_angle_1_deg 5.458 r_mcangle_it 2.015 r_mcbond_it 1.224 r_mcbond_other 1.223 r_angle_refined_deg 1.099 r_angle_other_deg 0.695 r_chiral_restr 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.487 r_dihedral_angle_4_deg 12.63 r_dihedral_angle_3_deg 11.527 r_dihedral_angle_1_deg 5.458 r_mcangle_it 2.015 r_mcbond_it 1.224 r_mcbond_other 1.223 r_angle_refined_deg 1.099 r_angle_other_deg 0.695 r_chiral_restr 0.065 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3656 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms 6
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing XSCALE data scaling REFMAC refinement XDS data reduction SHELXD phasing