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Crystal structure of a putative glycoside hydrolase (BVU_0362) from Bacteroides vulgatus ATCC 8482 at 1.80 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.67 293 0.01M nickel (II) chloride, 22.0% polyethylene glycol monomethyl ether 2000, 0.2M NDSB-256, 0.1M TRIS pH 8.67, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.87 57.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 226.439 α = 90 b = 67.684 β = 90 c = 90.066 γ = 90
Symmetry Space Group P 21 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 PIXEL DECTRIS PILATUS 6M Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2013-08-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.9792, 0.97868 SSRL BL11-1
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 1.8 29.211 95.4 0.075 7.89 3.74 127394 -3 21.082
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 1.8 1.86 89.8 0.563 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 1.8 29.211 127320 6400 98.67 0.1516 0.1501 0.1601 0.1796 0.1884 RANDOM 26.3603
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] -1.19 1.57 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.28 r_dihedral_angle_4_deg 15.522 r_dihedral_angle_3_deg 11.19 r_dihedral_angle_1_deg 6.675 r_mcangle_it 3.392 r_mcbond_it 2.577 r_mcbond_other 2.568 r_angle_refined_deg 1.6 r_angle_other_deg 1.121 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.28 r_dihedral_angle_4_deg 15.522 r_dihedral_angle_3_deg 11.19 r_dihedral_angle_1_deg 6.675 r_mcangle_it 3.392 r_mcbond_it 2.577 r_mcbond_other 2.568 r_angle_refined_deg 1.6 r_angle_other_deg 1.121 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8344 Nucleic Acid Atoms Solvent Atoms 1264 Heterogen Atoms 60
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing XSCALE data scaling REFMAC refinement XDS data reduction SHELXD phasing