5DIB

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4MPB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7295Protein: 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 coefficientSolvent content
2.9858.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 224.866α = 90
b = 102.633β = 104.83
c = 118.243γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.2529.7299.60.1429.43.712294630.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.2999.80.6492.053.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4mpb2.2529.72116530615499.50.217570.215570.25532RANDOM29.716
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]
4.250.4-0.48-3.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.296
r_dihedral_angle_4_deg9.339
r_dihedral_angle_3_deg8.758
r_dihedral_angle_1_deg1.934
r_angle_refined_deg1.769
r_angle_other_deg1.028
r_chiral_restr0.112
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_gen_planes_other0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.296
r_dihedral_angle_4_deg9.339
r_dihedral_angle_3_deg8.758
r_dihedral_angle_1_deg1.934
r_angle_refined_deg1.769
r_angle_other_deg1.028
r_chiral_restr0.112
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_gen_planes_other0.006
r_bond_other_d0.005
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 AtomsNumber
Protein Atoms15404
Nucleic Acid Atoms
Solvent Atoms867
Heterogen Atoms209

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building