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1.72 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) P449M point mutant from Staphylococcus aureus in complex with NAD+ and BME-modified Cys289
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MPB PDB entry 4MPB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 Protein: 7 mg/ml in 10 mM Tris-HCl, pH 8.3, 500 mM NaCl, 5 mM BME, 5 mM NAD. Crystallization: The Classics II Suite D3: 100 mM HEPES, pH 7.0, 30%(v/v) Jeffamine ED-2001. Cryo: crystallization condition
Crystal Properties Matthews coefficient Solvent content 2.94 58.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 224.271 α = 90 b = 102.721 β = 104.75 c = 117.81 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 MARMOSAIC 225 mm CCD 2015-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.72 30 99.2 0.079 15.3 3.7 271627 16.5
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 1.72 1.75 87.8 0.482 2.05 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4MPB 1.72 29.66 257471 13698 99.15 0.1647 0.16373 0.1741 0.18295 0.1905 RANDOM 17.824
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] 0.48 0.07 1.37 -1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.407 r_dihedral_angle_4_deg 15.782 r_dihedral_angle_3_deg 11.811 r_dihedral_angle_1_deg 4.696 r_angle_refined_deg 1.416 r_angle_other_deg 0.97 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.407 r_dihedral_angle_4_deg 15.782 r_dihedral_angle_3_deg 11.811 r_dihedral_angle_1_deg 4.696 r_angle_refined_deg 1.416 r_angle_other_deg 0.97 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15232 Nucleic Acid Atoms Solvent Atoms 2334 Heterogen Atoms 284
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling BLU-MAX data collection Coot model building ARP model building