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Crystal structure of putative glycoside hydrolase (YP_001304622.1) from Parabacteroides distasonis ATCC 8503 at 1.85 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 NANODROP, 20.0% PEG 3000, 0.1M Citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.12 42.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.209 α = 90 b = 84.915 β = 94.25 c = 77.991 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 mirror, vertical and horizontal focusing mirrors 2009-01-29 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.91162, 0.97954 SSRL BL12-2
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 1.85 29.604 100 0.093 0.093 9.4 3.8 66845 22.6
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 1.85 1.9 100 0.67 0.67 1.9 3.8 4946
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 1.85 29.604 66817 3384 99.97 0.171 0.169 0.1855 0.205 0.2124 RANDOM 16.106
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] 0.29 -1.03 1.67 -2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.483 r_dihedral_angle_4_deg 15.85 r_dihedral_angle_3_deg 12.338 r_dihedral_angle_1_deg 4.085 r_scangle_it 1.997 r_mcangle_it 1.704 r_angle_refined_deg 1.557 r_scbond_it 1.354 r_mcbond_it 1.085 r_angle_other_deg 0.966
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.483 r_dihedral_angle_4_deg 15.85 r_dihedral_angle_3_deg 12.338 r_dihedral_angle_1_deg 4.085 r_scangle_it 1.997 r_mcangle_it 1.704 r_angle_refined_deg 1.557 r_scbond_it 1.354 r_mcbond_it 1.085 r_angle_other_deg 0.966 r_mcbond_other 0.303 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6269 Nucleic Acid Atoms Solvent Atoms 415 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXD phasing autoSHARP phasing