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Crystal structure of a DUF4827 family protein (BDI_1692) from Parabacteroides distasonis ATCC 8503 at 2.40 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 277 1.0M lithium chloride, 20.0% polyethylene glycol 6000, 0.1M citric acid pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.04 59.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.266 α = 90 b = 92.266 β = 90 c = 112.85 γ = 90
Symmetry Space Group P 43 21 2
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) 2013-11-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97953,0.97903 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 2.4 29.673 96.7 0.058 12.07 19613 -3 66.457
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 2.39 2.48 76.6 0.664 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 MAD THROUGHOUT 2.4 29.673 19570 997 99.41 0.1863 0.1843 0.1955 0.2239 0.2383 RANDOM 70.8527
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] -1.45 -1.45 2.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.106 r_dihedral_angle_4_deg 16.774 r_dihedral_angle_3_deg 15.823 r_mcangle_it 7.403 r_dihedral_angle_1_deg 5.777 r_mcbond_other 5.736 r_mcbond_it 5.734 r_angle_refined_deg 1.368 r_angle_other_deg 0.851 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.106 r_dihedral_angle_4_deg 16.774 r_dihedral_angle_3_deg 15.823 r_mcangle_it 7.403 r_dihedral_angle_1_deg 5.777 r_mcbond_other 5.736 r_mcbond_it 5.734 r_angle_refined_deg 1.368 r_angle_other_deg 0.851 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2744 Nucleic Acid Atoms Solvent Atoms 117 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 autoSHARP phasing