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Crystal structure of a putative acetoin utilization protein (AcuB) from Vibrio cholerae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XKF PDB entry 1XKF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 294 100mM Tris pH 8.5, 2M ammonium phosphate, VAPOR DIFFUSION, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.03 39.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.677 α = 90 b = 58.006 β = 108.85 c = 53.561 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 77 IMAGE PLATE RIGAKU RAXIS IV Osmic mirrors 2006-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 20 98.3 0.073 0.073 23.8 7.8 22818 22430
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 84.8 0.481 0.481 2.8 5.4 1913
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 (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 1XKF 1.9 20 22816 22408 722 98.21 0.176 0.174 0.1745 0.234 0.2372 RANDOM 26.349
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] -0.59 0.61 0.26 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.633 r_dihedral_angle_4_deg 14.106 r_dihedral_angle_3_deg 12.293 r_dihedral_angle_1_deg 5.06 r_scangle_it 4.119 r_scbond_it 2.663 r_mcangle_it 1.771 r_angle_refined_deg 1.36 r_mcbond_it 1.189 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.633 r_dihedral_angle_4_deg 14.106 r_dihedral_angle_3_deg 12.293 r_dihedral_angle_1_deg 5.06 r_scangle_it 4.119 r_scbond_it 2.663 r_mcangle_it 1.771 r_angle_refined_deg 1.36 r_mcbond_it 1.189 r_nbtor_refined 0.301 r_symmetry_hbond_refined 0.259 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.196 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2078 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 35
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing