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Crystal structure of Putative exonuclease (RER070207002219) from Eubacterium rectale at 2.19 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.2000M MgCl2, 30.0000% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.48 50.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.248 α = 90 b = 88.248 β = 90 c = 69.35 γ = 120
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 collimating mirror, toroid focusing mirror 2009-05-14 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97936,0.97922 SSRL BL9-2
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 2.19 44.108 100 0.067 17.84 15931 -3 54.969
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 2.19 2.27 100 0.576 2
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 2.19 44.108 15916 793 99.97 0.21 0.208 0.2323 0.25 0.2648 RANDOM 26.641
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] 4.32 2.16 4.32 -6.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.353 r_dihedral_angle_3_deg 17.098 r_dihedral_angle_4_deg 15.778 r_dihedral_angle_1_deg 5.988 r_scangle_it 3.422 r_scbond_it 2.264 r_angle_refined_deg 1.561 r_mcangle_it 1.342 r_angle_other_deg 0.93 r_mcbond_it 0.728
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.353 r_dihedral_angle_3_deg 17.098 r_dihedral_angle_4_deg 15.778 r_dihedral_angle_1_deg 5.988 r_scangle_it 3.422 r_scbond_it 2.264 r_angle_refined_deg 1.561 r_mcangle_it 1.342 r_angle_other_deg 0.93 r_mcbond_it 0.728 r_mcbond_other 0.154 r_chiral_restr 0.092 r_bond_refined_d 0.018 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2119 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction autoSHARP phasing