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1.7 Angstrom Resolution Crystal Structure of Shikimate Kinase from Bacteroides thetaiotaomicron
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PT5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 Protein: 7.5 mg/mL, 0.25M Sodium chloride, Tris-HCl pH 8.3, Screen: Classics II (C9), 1.1M Sodium malonate, 0.1M HEPES pH 7.0, 0.5% (v/v) Jeffamine ED-2001, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.12 42.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.253 α = 90 b = 46.46 β = 97.42 c = 105.124 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 Beryllium lenses 2011-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.7 30 99.5 0.059 17.8 3.6 64576 64576 -3 25.8
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 1.7 1.73 93.8 0.495 2.09 2.6 3002
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 (All) 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 MOLECULAR REPLACEMENT THROUGHOUT 2PT5 1.7 29.06 61285 61285 3268 99.37 0.16527 0.16527 0.16348 0.1721 0.19923 0.2019 RANDOM 25.505
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] -0.06 -0.46 0.71 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.432 r_dihedral_angle_4_deg 17.745 r_dihedral_angle_3_deg 10.833 r_scangle_it 5.001 r_scbond_it 3.174 r_dihedral_angle_1_deg 3.125 r_mcangle_it 1.819 r_angle_refined_deg 1.287 r_mcbond_it 1.014 r_angle_other_deg 0.815
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.432 r_dihedral_angle_4_deg 17.745 r_dihedral_angle_3_deg 10.833 r_scangle_it 5.001 r_scbond_it 3.174 r_dihedral_angle_1_deg 3.125 r_mcangle_it 1.819 r_angle_refined_deg 1.287 r_mcbond_it 1.014 r_angle_other_deg 0.815 r_mcbond_other 0.349 r_chiral_restr 0.084 r_bond_refined_d 0.012 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 4295 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms 42
Software Software Software Name Purpose Blu-Ice data collection BALBES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling