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2.25 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) Y450L 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
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 Protein: BetB23 (Y450L mutant), 7 mg/ml in 10 mM Tris-HCl pH 8.3 500 mM NaCl 5 mM BME 5 mM NAD (co-crystallized)
Crystallization: on 11/19/2014; The Classics II Suite (D3): 0.1 M HEPES pH 7.0 30% (v/v) Jeffamine ED-2001; soaked in crystallization conditions for cryo protection.
Crystal Properties Matthews coefficient Solvent content 2.98 58.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 224.866 α = 90 b = 102.633 β = 104.83 c = 118.243 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 2.25 29.72 99.6 0.142 9.4 3.7 122946 30.3
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 2.25 2.29 99.8 0.649 2.05 3.6
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 4mpb 2.25 29.72 116530 6154 99.5 0.21757 0.21557 0.2173 0.25532 0.2545 RANDOM 29.716
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] 4.25 0.4 -0.48 -3.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.296 r_dihedral_angle_4_deg 9.339 r_dihedral_angle_3_deg 8.758 r_dihedral_angle_1_deg 1.934 r_angle_refined_deg 1.769 r_angle_other_deg 1.028 r_chiral_restr 0.112 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.296 r_dihedral_angle_4_deg 9.339 r_dihedral_angle_3_deg 8.758 r_dihedral_angle_1_deg 1.934 r_angle_refined_deg 1.769 r_angle_other_deg 1.028 r_chiral_restr 0.112 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.006 r_bond_other_d 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 15404 Nucleic Acid Atoms Solvent Atoms 867 Heterogen Atoms 209
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing Coot model building