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Crystal structure of the Bordetella bronchiseptica enzyme WbmG in complex with NAD and UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PZK PDB ENTRY 2PZK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M Hepes, 1.6 M (NH4)2SO4, 2 % (v/v) PEG 400, 10 mM UDP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.67 53.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.214 α = 90 b = 140.481 β = 90 c = 184.139 γ = 90
Symmetry Space Group C 2 2 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 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 2 30 99.9 0.085 19.6 5.9 51224 51158 2
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 2.03 100 0.773 2.28 5.9
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2PZK 2 30 51224 51115 2591 99.68 0.1708 0.1708 0.1711 0.221 RANDOM 28.315
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] 2.65 -1.3 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.944 r_dihedral_angle_3_deg 14.805 r_dihedral_angle_4_deg 14.188 r_dihedral_angle_1_deg 8.305 r_scangle_it 2.651 r_scbond_it 1.867 r_angle_refined_deg 1.7 r_mcangle_it 1.175 r_mcbond_it 0.75 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.944 r_dihedral_angle_3_deg 14.805 r_dihedral_angle_4_deg 14.188 r_dihedral_angle_1_deg 8.305 r_scangle_it 2.651 r_scbond_it 1.867 r_angle_refined_deg 1.7 r_mcangle_it 1.175 r_mcbond_it 0.75 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.239 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.187 r_chiral_restr 0.111 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4685 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling PHASER phasing