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Crystal structure of a Zn-dependent exopeptidase (BDI_3547) from Parabacteroides distasonis ATCC 8503 at 1.06 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1M bicine pH 9, 30% polyethylene glycol 6000, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.28 45.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.662 α = 105.74 b = 51.277 β = 99.92 c = 72.985 γ = 97.46
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 Vertical focusing mirror; double crystal Si(111) monochromator 2011-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 SSRL BL14-1
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 1.06 25.382 91.6 0.056 11.71 252314 -3 8.483
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 1.06 1.1 87.9 0.881 1.6
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 1.06 25.382 252112 12723 92.09 0.1126 0.1115 0.1249 0.1315 0.1429 RANDOM 15.0206
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] -0.03 -0.06 -0.49 -0.51 0.1 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.49 r_dihedral_angle_4_deg 22.505 r_dihedral_angle_3_deg 11.9 r_sphericity_free 9.787 r_dihedral_angle_1_deg 5.72 r_scangle_it 4.417 r_sphericity_bonded 4.035 r_scbond_it 3.076 r_mcangle_it 2.389 r_mcbond_it 1.693
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.49 r_dihedral_angle_4_deg 22.505 r_dihedral_angle_3_deg 11.9 r_sphericity_free 9.787 r_dihedral_angle_1_deg 5.72 r_scangle_it 4.417 r_sphericity_bonded 4.035 r_scbond_it 3.076 r_mcangle_it 2.389 r_mcbond_it 1.693 r_angle_refined_deg 1.652 r_rigid_bond_restr 1.495 r_angle_other_deg 0.959 r_mcbond_other 0.761 r_chiral_restr 0.109 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4557 Nucleic Acid Atoms Solvent Atoms 1058 Heterogen Atoms 22
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