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2.35 Angstrom resolution structure of WecB (VC0917), a UDP-N-acetylglucosamine 2-epimerase from Vibrio cholerae.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F6D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 1:1 V/V. Protein solution: 7.9mG/mL of protein, 0.5M NaCl, 10mM TRIS-HCL, 10 mM UDP.
Reservoir solution (PACT, #23): 0.2M Calcium chloride, 0.1M MES, 20% w/v PEG 6000,
pH 6.0, Vapor Diffusion, sitting drop, Temp. 295K., VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.7 54.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.391 α = 90 b = 88.127 β = 90 c = 132.193 γ = 90
Symmetry Space Group P 21 21 21
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 2008-07-25 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 2.35 30 100 0.095 17.9 6.6 40522 40522 -3 47.9
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 2.35 2.43 100 0.426 3.9 5.5 3962
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 1F6D 2.35 30 38263 38263 2012 99.93 0.17542 0.17542 0.17238 0.1735 0.23376 0.2344 RANDOM 43.448
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] -1.68 1.02 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.559 r_dihedral_angle_4_deg 11.303 r_dihedral_angle_3_deg 9.762 r_scangle_it 4.746 r_scbond_it 3.109 r_dihedral_angle_1_deg 2.351 r_mcangle_it 2.098 r_angle_refined_deg 1.612 r_mcbond_it 1.278 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.559 r_dihedral_angle_4_deg 11.303 r_dihedral_angle_3_deg 9.762 r_scangle_it 4.746 r_scbond_it 3.109 r_dihedral_angle_1_deg 2.351 r_mcangle_it 2.098 r_angle_refined_deg 1.612 r_mcbond_it 1.278 r_nbtor_refined 0.3 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.196 r_xyhbond_nbd_refined 0.172 r_symmetry_hbond_refined 0.124 r_chiral_restr 0.11 r_metal_ion_refined 0.06 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5772 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing