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1.2 Angstrom structure of the exonuclease III homologue Mth0212
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FZI PDB ENTRY 3FZI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 reservoir solution: 20% (v/v) MPD, 40mM MgAc, 50mM sodium cacodylate pH 6.0; protein solution: 180mM KCl, 10mM KH2PO4/K2HPO4 pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.33 α = 90 b = 72.11 β = 117.96 c = 46.33 γ = 90
Symmetry Space Group P 1 21 1
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 225 mm CCD 2008-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
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 1.23 18 97.9 0.029 28.1 4.1 73200 -3 15.044
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) 1.23 1.27 92.7 0.131 9 3.6 6790
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3FZI 1.23 9.99 73130 69444 3686 93.14 0.1222 0.1212 0.1718 random 20.046
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 29 2606.71
RMS Deviations Key Refinement Restraint Deviation s_from_restr_planes 0.384 s_approx_iso_adps 0.088 s_non_zero_chiral_vol 0.087 s_anti_bump_dis_restr 0.08 s_zero_chiral_vol 0.069 s_similar_adp_cmpnt 0.048 s_angle_d 0.031 s_bond_d 0.019 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2168 Nucleic Acid Atoms Solvent Atoms 433 Heterogen Atoms 32
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXL-97 refinement