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2.2 Angstrom Resolution Crystal Structure of putative UDP-N-acetylglucosamine 2-epimerase from Listeria monocytogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BEO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 295 Protein: 7.4mGr/mL, 0.5 Sodium cloride, 0.01M Tris-HCl pH 8.3; Screen: PEGs II (H1), 0.01M tri-Sodium citrate, 33% (w/v) PEG6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.91 35.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.19 α = 90 b = 84.405 β = 90.07 c = 100.461 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 2010-07-19 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 2.2 30 99.5 0.046 22.4 3 67586 67586 -3 52.9
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) 2.2 2.24 99.8 0.523 2.06 2.9 3349
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 3BEO 2.2 29.59 64131 64131 3414 98.06 0.18967 0.18967 0.18724 0.1904 0.23474 0.2366 RANDOM 47.288
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] 2.52 -1.88 -1.41 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.737 r_dihedral_angle_4_deg 8.49 r_dihedral_angle_3_deg 8.403 r_scangle_it 3.891 r_scbond_it 2.525 r_dihedral_angle_1_deg 1.901 r_mcangle_it 1.481 r_angle_refined_deg 1.378 r_mcbond_it 0.84 r_angle_other_deg 0.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.737 r_dihedral_angle_4_deg 8.49 r_dihedral_angle_3_deg 8.403 r_scangle_it 3.891 r_scbond_it 2.525 r_dihedral_angle_1_deg 1.901 r_mcangle_it 1.481 r_angle_refined_deg 1.378 r_mcbond_it 0.84 r_angle_other_deg 0.825 r_mcbond_other 0.227 r_chiral_restr 0.071 r_bond_refined_d 0.009 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 11700 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 17
Software Software Software Name Purpose Blu-Ice data collection BALBES phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling