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Crystal structure of a SusD superfamily protein (BDI_3964) from Parabacteroides distasonis ATCC 8503 at 1.95 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.17M sodium acetate, 25.3% polyethylene glycol 4000, 15.0% Glycerol, 0.1M TRIS pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.74 α = 90 b = 92.479 β = 90 c = 152.104 γ = 90
Symmetry Space Group P 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 2010-07-23 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97918,0.97896 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 29.37 99.2 0.123 7.7 3.8 76628 76628 20.344
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 1.95 2 100 0.699 0.699 2 3.7 5660
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 1.95 29.37 76591 3860 98.82 0.146 0.1436 0.1542 0.1906 0.1981 RANDOM 27.8721
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] 0.71 -0.68 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.73 r_dihedral_angle_4_deg 18.006 r_dihedral_angle_3_deg 11.968 r_scangle_it 6.1 r_dihedral_angle_1_deg 5.32 r_scbond_it 4.553 r_mcangle_it 2.808 r_mcbond_it 1.8 r_angle_refined_deg 1.451 r_angle_other_deg 1.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.73 r_dihedral_angle_4_deg 18.006 r_dihedral_angle_3_deg 11.968 r_scangle_it 6.1 r_dihedral_angle_1_deg 5.32 r_scbond_it 4.553 r_mcangle_it 2.808 r_mcbond_it 1.8 r_angle_refined_deg 1.451 r_angle_other_deg 1.088 r_mcbond_other 0.522 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7591 Nucleic Acid Atoms Solvent Atoms 847 Heterogen Atoms 148
Software Software Software Name Purpose SOLVE phasing REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction