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Crystal structure of a mutT/nudix family protein from Listeria innocua
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 294 100mM Hepes pH 7.5, 4% glycerol, 1.3M tri-sodium citrate, vapor diffusion, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.11 60.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.129 α = 90 b = 96.129 β = 90 c = 97.594 γ = 120
Symmetry Space Group P 65 2 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 CCD MARMOSAIC 225 mm CCD 2009-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97958 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 31.668 99.9 0.105 0.105 26.4 42.4 14089 14075 38.9
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 2.2 2.32 100 0.449 0.449 9.9 43.3 2001
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.2 20 14030 14015 685 99.89 0.225 0.223 0.2242 0.276 0.2785 RANDOM 50.271
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] -3.73 -1.87 -3.73 5.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.639 r_dihedral_angle_3_deg 18.367 r_dihedral_angle_4_deg 11.085 r_dihedral_angle_1_deg 6.776 r_scangle_it 4.408 r_scbond_it 2.669 r_mcangle_it 2.056 r_angle_refined_deg 1.653 r_mcbond_it 1.122 r_angle_other_deg 0.992
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.639 r_dihedral_angle_3_deg 18.367 r_dihedral_angle_4_deg 11.085 r_dihedral_angle_1_deg 6.776 r_scangle_it 4.408 r_scbond_it 2.669 r_mcangle_it 2.056 r_angle_refined_deg 1.653 r_mcbond_it 1.122 r_angle_other_deg 0.992 r_mcbond_other 0.215 r_chiral_restr 0.094 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1206 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 6
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXCD phasing SHELXE model building