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Crystal structure of the Bordetella bronchiseptica enzyme WbmH in complex with NAD+
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, SITTING DROP 7.5 293 0.1 M Hepes, 10 % (v/v) isopropanol, 20 % (w/v) PEG 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 46.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.673 α = 90 b = 158.988 β = 90 c = 68.222 γ = 90
Symmetry Space Group P 21 21 2
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 4 2004-12-04 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 4 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.934 ESRF ID29 2 SYNCHROTRON SRS BEAMLINE PX14.1 1.488 SRS PX14.1
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 2.19 30 93.9 0.114 15.2 5.22 53222 49975 3
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 2.2 2.25 91.3 0.38 3.63 3.58
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 ENTRY 2PZK 2.19 30 3.5 53222 47385 2559 93.2 0.179 0.17866 0.17609 0.173 0.22679 0.2222 RANDOM 28.505
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] 0.82 0.77 -1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.632 r_dihedral_angle_4_deg 20.14 r_dihedral_angle_3_deg 14.418 r_dihedral_angle_1_deg 6.044 r_scangle_it 3.005 r_scbond_it 2.08 r_angle_refined_deg 1.513 r_mcangle_it 1.331 r_mcbond_it 0.874 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.632 r_dihedral_angle_4_deg 20.14 r_dihedral_angle_3_deg 14.418 r_dihedral_angle_1_deg 6.044 r_scangle_it 3.005 r_scbond_it 2.08 r_angle_refined_deg 1.513 r_mcangle_it 1.331 r_mcbond_it 0.874 r_nbtor_refined 0.306 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.177 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6812 Nucleic Acid Atoms Solvent Atoms 415 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling PHASER phasing