☰ Navigation Tabs
Crystal structure of putative glucoamylase (YP_210071.1) from Bacteroides fragilis NCTC 9343 at 2.12 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 15.8% polyethylene glycol 3350, 0.1M potassium fluoride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.35 47.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.18 α = 90 b = 71.76 β = 92.3 c = 221.79 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 MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2008-08-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97929,0.97920 SSRL BL9-2
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 2.12 29.591 90.7 0.09 5.54 102011 -3 24.102
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 2.12 2.2 84.4 0.409 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 2.12 29.591 101993 5086 98.12 0.161 0.158 0.163 0.213 0.2132 RANDOM 26.572
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] 0.18 -0.16 0.91 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.24 r_dihedral_angle_3_deg 13.407 r_dihedral_angle_4_deg 12.918 r_dihedral_angle_1_deg 5.999 r_scangle_it 5.629 r_scbond_it 4.196 r_mcangle_it 2.275 r_angle_refined_deg 1.396 r_mcbond_it 1.351 r_angle_other_deg 0.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.24 r_dihedral_angle_3_deg 13.407 r_dihedral_angle_4_deg 12.918 r_dihedral_angle_1_deg 5.999 r_scangle_it 5.629 r_scbond_it 4.196 r_mcangle_it 2.275 r_angle_refined_deg 1.396 r_mcbond_it 1.351 r_angle_other_deg 0.939 r_mcbond_other 0.496 r_symmetry_vdw_other 0.246 r_symmetry_vdw_refined 0.216 r_nbd_refined 0.207 r_nbd_other 0.194 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.183 r_symmetry_hbond_refined 0.177 r_metal_ion_refined 0.148 r_nbtor_other 0.086 r_chiral_restr 0.082 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13458 Nucleic Acid Atoms Solvent Atoms 1246 Heterogen Atoms 342
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing