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Crystal structure of a glycoside hydrolase family 33, candidate sialidase (BDI_2946) from Parabacteroides distasonis ATCC 8503 at 1.90 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10.5 277 0.2M lithium sulfate, 1.2M sodium dihydrogen phosphate, 0.8M di-potassium hydrogen phosphate, 0.1M Glycine pH 10.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.94 58.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.738 α = 90 b = 171.738 β = 90 c = 243.786 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 PIXEL DECTRIS PILATUS 6M Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2012-04-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97922,0.91837,0.97871 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.9 29.773 95.9 0.105 0.143 6.44 209534 -3 19.77
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 94.7 0.619 0.85 1.4
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 1.9 29.773 209495 10526 99.09 0.2088 0.207 0.2119 0.2426 0.2451 RANDOM 27.3971
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] 0.21 0.1 0.21 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.349 r_dihedral_angle_4_deg 10.873 r_dihedral_angle_3_deg 10.521 r_dihedral_angle_1_deg 4.873 r_angle_refined_deg 1.531 r_angle_other_deg 0.999 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.349 r_dihedral_angle_4_deg 10.873 r_dihedral_angle_3_deg 10.521 r_dihedral_angle_1_deg 4.873 r_angle_refined_deg 1.531 r_angle_other_deg 0.999 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16160 Nucleic Acid Atoms Solvent Atoms 2000 Heterogen Atoms 178
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