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Crystal structure of a putative secreted protein (BDI_1231) from Parabacteroides distasonis ATCC 8503 at 2.00 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 30.0% polyethylene glycol 4000, 0.2M magnesium chloride, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.58 52.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.746 α = 91.64 b = 65.323 β = 92.35 c = 78.756 γ = 104.5
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) 2012-08-02 M SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 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 1.87 48.317 87.2 0.059 11.4 53817 -3 30.595
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 1.87 1.94 61.5 0.57 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 SAD THROUGHOUT 1.87 48.317 53272 2703 86.62 0.1984 0.1963 0.2036 0.2382 0.2439 RANDOM 42.5108
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] -0.56 0.85 -0.47 3.15 0.1 -3.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.903 r_dihedral_angle_4_deg 18.507 r_dihedral_angle_3_deg 12.165 r_dihedral_angle_1_deg 6.637 r_angle_refined_deg 1.479 r_angle_other_deg 0.872 r_chiral_restr 0.045 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.903 r_dihedral_angle_4_deg 18.507 r_dihedral_angle_3_deg 12.165 r_dihedral_angle_1_deg 6.637 r_angle_refined_deg 1.479 r_angle_other_deg 0.872 r_chiral_restr 0.045 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4836 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms
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