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Crystal structure of a putative glycosyl hydrolase (BDI_3914) from Parabacteroides distasonis ATCC 8503 at 2.13 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 277 0.2M magnesium acetate, 20.0% polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.5 50.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.774 α = 90 b = 144.763 β = 101.27 c = 82.452 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 PIXEL DECTRIS PILATUS 6M Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2013-11-27 M MAD 2 1 x-ray 100 CCD MARMOSAIC 325 mm CCD double crystal monochromator 2014-02-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97895 SSRL BL11-1 2 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97941 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 2.13 48.254 95 0.111 6.96 58318 -3 26.92
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 2.13 2.21 96.6 0.477 2.1
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 2.13 48.254 55339 2948 95.03 0.1724 0.1707 0.181 0.2035 0.2097 RANDOM 27.0401
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] 1.21 0.74 -0.3 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.614 r_dihedral_angle_3_deg 10.459 r_dihedral_angle_4_deg 8.503 r_dihedral_angle_1_deg 6.98 r_mcangle_it 2.045 r_mcbond_it 1.378 r_mcbond_other 1.378 r_angle_refined_deg 1.199 r_angle_other_deg 0.775 r_chiral_restr 0.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.614 r_dihedral_angle_3_deg 10.459 r_dihedral_angle_4_deg 8.503 r_dihedral_angle_1_deg 6.98 r_mcangle_it 2.045 r_mcbond_it 1.378 r_mcbond_other 1.378 r_angle_refined_deg 1.199 r_angle_other_deg 0.775 r_chiral_restr 0.041 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7530 Nucleic Acid Atoms Solvent Atoms 910 Heterogen Atoms 16
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SOLVE phasing REFMAC refinement XDS data reduction XSCALE data scaling