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Crystal structure of Putative glycosyl hydrolase (YP_001301887.1) from Parabacteroides distasonis ATCC 8503 at 2.00 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 0.2000M NaCl, 30.0000% PEG-3000, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.09 41.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.404 α = 90 b = 45.404 β = 90 c = 241.069 γ = 120
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) 2009-04-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91162,0.97805,0.97874 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 28.105 99.7 0.078 0.078 9.7 2.9 37531 26.958
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 2 2.05 96.9 0.368 0.368 2.2 2.5 2709
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 28.105 37453 1876 99.73 0.166 0.163 0.1685 0.222 0.2259 RANDOM 31.58
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] 1.59 0.79 1.59 -2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.094 r_dihedral_angle_4_deg 17.677 r_dihedral_angle_3_deg 14.292 r_dihedral_angle_1_deg 7.051 r_scangle_it 3.681 r_scbond_it 2.769 r_mcangle_it 2.204 r_angle_refined_deg 1.529 r_mcbond_it 1.492 r_angle_other_deg 0.918
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.094 r_dihedral_angle_4_deg 17.677 r_dihedral_angle_3_deg 14.292 r_dihedral_angle_1_deg 7.051 r_scangle_it 3.681 r_scbond_it 2.769 r_mcangle_it 2.204 r_angle_refined_deg 1.529 r_mcbond_it 1.492 r_angle_other_deg 0.918 r_mcbond_other 0.688 r_symmetry_vdw_other 0.277 r_nbd_refined 0.214 r_nbd_other 0.193 r_symmetry_vdw_refined 0.189 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.154 r_symmetry_hbond_refined 0.133 r_metal_ion_refined 0.117 r_chiral_restr 0.098 r_nbtor_other 0.088 r_bond_refined_d 0.015 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 4669 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction