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Crystal structure of a glycosyl hydrolase (BT_2959) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.11 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 277 15.0000% Glycerol, 0.1700M NH4OAc, 25.5000% PEG-4000, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.58 52.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.923 α = 90 b = 78.923 β = 90 c = 166.87 γ = 90
Symmetry Space Group P 43 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2009-04-16 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97852,0.97802 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.11 29.801 99.9 0.119 0.119 10.9 6.3 31222 35.599
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) 2.11 2.16 100 0.923 0.923 1.8 6.4 2248
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.11 29.801 31147 1564 99.85 0.197 0.195 0.238 0.2178 RANDOM 47.063
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] 1.65 1.65 -3.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.437 r_dihedral_angle_4_deg 14.915 r_dihedral_angle_3_deg 10.865 r_scangle_it 5.238 r_scbond_it 3.921 r_dihedral_angle_1_deg 3.69 r_mcangle_it 2.293 r_angle_refined_deg 1.523 r_mcbond_it 1.299 r_angle_other_deg 0.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.437 r_dihedral_angle_4_deg 14.915 r_dihedral_angle_3_deg 10.865 r_scangle_it 5.238 r_scbond_it 3.921 r_dihedral_angle_1_deg 3.69 r_mcangle_it 2.293 r_angle_refined_deg 1.523 r_mcbond_it 1.299 r_angle_other_deg 0.848 r_mcbond_other 0.289 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3444 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing