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Crystal structure of a putative dipeptidyl-peptidase VI (BACOVA_00612) from Bacteroides ovatus at 1.72 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 15.000000000% Glycerol, 0.170000000M NaOAc, 25.500000000% PEG-4000, 0.1M TRIS pH 8.5, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.1 41.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.136 α = 90 b = 62.495 β = 90 c = 156.809 γ = 90
Symmetry Space Group P 21 21 21
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 collimating mirror, toroid focusing mirror 2010-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 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 1.72 48.87 100 0.125 11.06 6.96 63712 -3 16.41
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) 1.72 1.78 100 0.797 2.2
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 SAD THROUGHOUT 1.72 48.87 63635 2823 99.98 0.1424 0.141 0.1497 0.1712 0.178 RANDOM 18.5442
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 0.68 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.518 r_dihedral_angle_4_deg 16.171 r_dihedral_angle_3_deg 11.548 r_dihedral_angle_1_deg 6.36 r_scangle_it 5.721 r_scbond_it 3.735 r_mcangle_it 2.186 r_angle_refined_deg 1.458 r_mcbond_it 1.369 r_angle_other_deg 0.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.518 r_dihedral_angle_4_deg 16.171 r_dihedral_angle_3_deg 11.548 r_dihedral_angle_1_deg 6.36 r_scangle_it 5.721 r_scbond_it 3.735 r_mcangle_it 2.186 r_angle_refined_deg 1.458 r_mcbond_it 1.369 r_angle_other_deg 0.935 r_mcbond_other 0.527 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4779 Nucleic Acid Atoms Solvent Atoms 786 Heterogen Atoms 68
Software Software Software Name Purpose SHELX phasing REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing