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2.85 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) H448F/P449M double mutant from Staphylococcus aureus in complex with NAD+ and BME-free 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 8.5 295 Crystallization: The Classics II Suite G5: 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 25% (w/v) PEG 3350. Protein: 5 mg/ml in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 0.5 mM TCEP, 5 mM NAD+. Cryo: crystallization condition
Crystal Properties Matthews coefficient Solvent content 2.3 46.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.998 α = 90 b = 168.999 β = 104.51 c = 144.467 γ = 90
Symmetry Space Group P 1 21 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 300 mm CCD 2014-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.85 30 100 0.117 11.9 3.8 96507 64.4
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 2.85 2.9 100 0.683 2 3.9
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 2.85 29.89 91344 4864 99.85 0.16666 0.16422 0.1663 0.21253 0.2093 RANDOM 55.333
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] -2.53 -0.06 -0.51 2.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.35 r_dihedral_angle_4_deg 11.31 r_dihedral_angle_3_deg 10.095 r_dihedral_angle_1_deg 2.156 r_angle_refined_deg 1.615 r_angle_other_deg 1.098 r_chiral_restr 0.097 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.35 r_dihedral_angle_4_deg 11.31 r_dihedral_angle_3_deg 10.095 r_dihedral_angle_1_deg 2.156 r_angle_refined_deg 1.615 r_angle_other_deg 1.098 r_chiral_restr 0.097 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.005 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 30833 Nucleic Acid Atoms Solvent Atoms 420 Heterogen Atoms 427
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing