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Crystal structure of the Bordetella bronchiseptica enzyme WbmF in complex with NAD+ and UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BXK PDB ENTRIES 1BXK, 1KEU, 1R6D experimental model PDB 1KEU PDB ENTRIES 1BXK, 1KEU, 1R6D experimental model PDB 1R6D PDB ENTRIES 1BXK, 1KEU, 1R6D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 0.1 M bicine, 16 % (w/w) PEG 8000.
UDP was added by soaking prior to cryo-protection., pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.442 α = 90 b = 78.119 β = 108.08 c = 59.262 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 ADSC QUANTUM 315 2006-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.977 ESRF ID14-4
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 1.75 50 93.3 0.049 23.7 3.9 36325 33895 2 25.8
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 1.75 1.78 62.6 0.337 2.38 2.4 1137
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRIES 1BXK, 1KEU, 1R6D 1.75 28.52 36325 33887 1677 93.23 0.183 0.18302 0.183 0.1807 0.219 RANDOM 40.4
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] 0.01 -1.1 1.55 -2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.575 r_dihedral_angle_4_deg 22.06 r_dihedral_angle_3_deg 14.653 r_dihedral_angle_1_deg 14.078 r_scangle_it 2.705 r_scbond_it 1.902 r_angle_refined_deg 1.746 r_mcangle_it 1.278 r_mcbond_it 0.825 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.575 r_dihedral_angle_4_deg 22.06 r_dihedral_angle_3_deg 14.653 r_dihedral_angle_1_deg 14.078 r_scangle_it 2.705 r_scbond_it 1.902 r_angle_refined_deg 1.746 r_mcangle_it 1.278 r_mcbond_it 0.825 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.223 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.122 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2544 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling PHASER phasing