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Crystal structure of PUTATIVE SUGAR HYDROLASE (YP_001304206.1) from Parabacteroides distasonis ATCC 8503 at 1.59 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.2000M Na2Ci, 30.0000% PEG-400, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.44 49.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.259 α = 90 b = 117.259 β = 90 c = 118.068 γ = 90
Symmetry Space Group P 43 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 CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2009-02-18 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97905,0.97839 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 1.59 29.311 96.6 0.064 16.59 107246 -3 23.046
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 1.59 1.65 98.5 0.01 1.8
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 1.59 29.311 107212 5379 96.62 0.17 0.17 0.1806 0.185 0.1918 RANDOM 36.734
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] 0.43 0.43 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.999 r_dihedral_angle_4_deg 14.754 r_dihedral_angle_3_deg 12.857 r_dihedral_angle_1_deg 6.542 r_scangle_it 4.407 r_scbond_it 3.103 r_mcangle_it 1.963 r_angle_refined_deg 1.561 r_angle_other_deg 1.32 r_mcbond_it 1.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.999 r_dihedral_angle_4_deg 14.754 r_dihedral_angle_3_deg 12.857 r_dihedral_angle_1_deg 6.542 r_scangle_it 4.407 r_scbond_it 3.103 r_mcangle_it 1.963 r_angle_refined_deg 1.561 r_angle_other_deg 1.32 r_mcbond_it 1.188 r_mcbond_other 0.373 r_symmetry_hbond_refined 0.196 r_symmetry_vdw_refined 0.19 r_nbtor_refined 0.179 r_nbd_refined 0.177 r_xyhbond_nbd_refined 0.166 r_nbd_other 0.157 r_symmetry_vdw_other 0.135 r_chiral_restr 0.099 r_nbtor_other 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5418 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing