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1.45 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes in Complex with Shikimate and NAD.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NPD pdb entry 1NPD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 Protein: 7.5mG/mL, 0.25M Sodium chloride, 0.01M TRIS-HCl (pH 8.3), 1mM Shikimate;
Screen: PEG's (D2), 0.1M HEPES (pH 7.5), 25% (w/v) PEG 4000. , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.16 42.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.851 α = 90 b = 82.878 β = 90.03 c = 101.26 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 300 mm CCD Beryllium lenses 2011-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.45 30 96.7 0.055 20.6 3.8 203043 203043 -3 17.9
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 1.45 1.48 89.4 0.34 3.1 3.4 9339
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 pdb entry 1NPD 1.45 29.31 192681 192681 10155 96.68 0.15011 0.15011 0.14871 0.1556 0.17645 0.1812 RANDOM 15.508
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] -1.26 1.23 1.72 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.385 r_dihedral_angle_4_deg 12.325 r_dihedral_angle_3_deg 9.119 r_scangle_it 4.708 r_dihedral_angle_1_deg 3.872 r_scbond_it 2.922 r_mcangle_it 1.761 r_angle_refined_deg 1.607 r_mcbond_it 1.079 r_angle_other_deg 0.898
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.385 r_dihedral_angle_4_deg 12.325 r_dihedral_angle_3_deg 9.119 r_scangle_it 4.708 r_dihedral_angle_1_deg 3.872 r_scbond_it 2.922 r_mcangle_it 1.761 r_angle_refined_deg 1.607 r_mcbond_it 1.079 r_angle_other_deg 0.898 r_mcbond_other 0.382 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8944 Nucleic Acid Atoms Solvent Atoms 1907 Heterogen Atoms 204
Software Software Software Name Purpose Blu-Ice data collection BALBES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling