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2.45 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Campylobacter jejuni.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BQ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 Protein: 7.7 mg/ml, 0.25M Sodium chloride, 0.01M Tris HCl (pH 8.3);
Screen: PEG II (D1), 0.1M Sodium acetate, 0.1 HEPES (pH 7.5), 22% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.14 42.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.258 α = 90 b = 86.024 β = 109.28 c = 80.421 γ = 90
Symmetry Space Group C 1 2 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 C(111) 2009-06-18 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) R Sym I (Observed) Rrim I (All) 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 2.45 30 98.6 0.075 0.075 0.045 15.2 3.7 29963 -3 56.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.49 87.7 0.538 0.538 0.34 0.77 2.1 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT 5BQ2 2.46 29.93 28521 1442 97.84 0.22661 0.22426 0.2237 0.27456 0.2743 RANDOM 56.486
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] 3.5 -6.15 -0.36 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.359 r_dihedral_angle_3_deg 10.238 r_dihedral_angle_4_deg 8.352 r_long_range_B_refined 6.439 r_long_range_B_other 6.421 r_mcangle_it 2.614 r_mcangle_other 2.613 r_scangle_other 2.428 r_dihedral_angle_1_deg 2.103 r_mcbond_it 1.506
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.359 r_dihedral_angle_3_deg 10.238 r_dihedral_angle_4_deg 8.352 r_long_range_B_refined 6.439 r_long_range_B_other 6.421 r_mcangle_it 2.614 r_mcangle_other 2.613 r_scangle_other 2.428 r_dihedral_angle_1_deg 2.103 r_mcbond_it 1.506 r_mcbond_other 1.506 r_angle_refined_deg 1.445 r_scbond_it 1.427 r_scbond_other 1.426 r_angle_other_deg 0.894 r_chiral_restr 0.081 r_gen_planes_refined 0.023 r_gen_planes_other 0.021 r_bond_refined_d 0.009 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6427 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing