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Crystal structure of a DUF3836 family protein (BDI_3222) from Parabacteroides distasonis ATCC 8503 at 1.50 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 277 40.00% 2-methyl-2,4-pentanediol, 0.1M phosphate-citrate pH 4.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.29 62.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.001 α = 90 b = 71.697 β = 90 c = 82.683 γ = 90
Symmetry Space Group I 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 Vertical focusing mirror; double crystal Si(111) monochromator 2014-06-10 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 0.95369,0.97934,0.97907 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 1.5 27.084 98.2 0.045 14.96 27948 -3 18.114
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 1.5 1.6 91.2 0.483 1.9
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 1.5 27.084 26540 1407 98.15 0.1675 0.1664 0.1661 0.1876 0.1882 RANDOM 22.887
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] 0.14 0.25 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.862 r_dihedral_angle_3_deg 11.53 r_dihedral_angle_4_deg 9.996 r_dihedral_angle_1_deg 6.173 r_mcangle_it 3.077 r_mcbond_it 1.924 r_mcbond_other 1.912 r_angle_refined_deg 1.736 r_angle_other_deg 0.784 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.862 r_dihedral_angle_3_deg 11.53 r_dihedral_angle_4_deg 9.996 r_dihedral_angle_1_deg 6.173 r_mcangle_it 3.077 r_mcbond_it 1.924 r_mcbond_other 1.912 r_angle_refined_deg 1.736 r_angle_other_deg 0.784 r_chiral_restr 0.115 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 925 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 31
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