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Crystal structure of the Bordetella bronchiseptica enzyme WbmF in complex with NAD+
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, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.884 α = 90 b = 77.875 β = 108.17 c = 59.226 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 1.9 50 96.6 0.039 32.1 4.6 28232 27275 5 24.88
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 1.9 1.93 77.4 0.223 5.89 3 1061
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 PDB entries 1BXK, 1KEU, 1R6D 1.9 38.38 28232 25919 1352 96.48 0.163 0.16305 0.16086 0.1661 0.20428 0.2093 RANDOM 23.931
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] 0.31 -0.73 1.12 -1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.072 r_dihedral_angle_4_deg 20.746 r_dihedral_angle_3_deg 14.511 r_dihedral_angle_1_deg 6.084 r_scangle_it 2.324 r_scbond_it 1.629 r_angle_refined_deg 1.458 r_angle_other_deg 1.003 r_mcangle_it 0.913 r_mcbond_it 0.651
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.072 r_dihedral_angle_4_deg 20.746 r_dihedral_angle_3_deg 14.511 r_dihedral_angle_1_deg 6.084 r_scangle_it 2.324 r_scbond_it 1.629 r_angle_refined_deg 1.458 r_angle_other_deg 1.003 r_mcangle_it 0.913 r_mcbond_it 0.651 r_symmetry_vdw_other 0.257 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.21 r_nbd_other 0.196 r_mcbond_other 0.176 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.174 r_symmetry_hbond_refined 0.153 r_chiral_restr 0.087 r_xyhbond_nbd_other 0.087 r_nbtor_other 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2519 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling PHASER phasing