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Crystal structure of putative adhesin (YP_001304413.1) from Parabacteroides distasonis ATCC 8503 at 2.41 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 22.0000% polyethylene glycol 6000, 1.0000M lithium chloride, 0.1M TRIS pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.72 54.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.951 α = 90 b = 55.33 β = 105.4 c = 120.613 γ = 90
Symmetry Space Group P 1 2 1
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) 2009-07-07 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97925,0.97876 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.41 29.761 98.1 0.07 0.07 10.8 2.9 32190 53.817
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.41 2.47 83.6 0.598 0.598 1.6 2.2 1995
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 2.41 29.761 32190 1628 97.55 0.191 0.189 0.1912 0.225 0.2244 RANDOM 49.559
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] -1.71 -0.25 1.33 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.018 r_dihedral_angle_4_deg 18.239 r_dihedral_angle_3_deg 15.598 r_dihedral_angle_1_deg 7.233 r_scangle_it 4.028 r_scbond_it 2.961 r_mcangle_it 2.181 r_angle_refined_deg 1.513 r_mcbond_it 1.411 r_angle_other_deg 0.903
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.018 r_dihedral_angle_4_deg 18.239 r_dihedral_angle_3_deg 15.598 r_dihedral_angle_1_deg 7.233 r_scangle_it 4.028 r_scbond_it 2.961 r_mcangle_it 2.181 r_angle_refined_deg 1.513 r_mcbond_it 1.411 r_angle_other_deg 0.903 r_mcbond_other 0.305 r_symmetry_vdw_other 0.264 r_symmetry_vdw_refined 0.236 r_symmetry_hbond_refined 0.209 r_nbd_other 0.204 r_nbd_refined 0.201 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.087 r_nbtor_other 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5303 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction