4QN2

2.6 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) G234S mutant from Staphylococcus aureus (IDP00699) in complex with NAD+ and BME-free Cys289


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52957 mg/mL protein in 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 0.5 mM TCEP, 2 mM NAD+, crystallization: The Classics II Suite (G9): 0.2 M ammonium acetate, 0.1 M Tris, pH 8.5, 25% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2846.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.592α = 90
b = 168.368β = 104.92
c = 144.523γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDberyllium lenses2013-10-14MSINGLE 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
12.63093.70.10412.83.9117959117959-351.9
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)
12.62.6497.10.6072.343.86068

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4MPB2.629.78111581111581591693.610.186050.184270.21925RANDOM42.282
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]
-3.83-1.07-2.485.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.843
r_dihedral_angle_3_deg11.426
r_dihedral_angle_4_deg10.629
r_dihedral_angle_1_deg2.531
r_angle_refined_deg1.587
r_angle_other_deg1.136
r_chiral_restr0.097
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.843
r_dihedral_angle_3_deg11.426
r_dihedral_angle_4_deg10.629
r_dihedral_angle_1_deg2.531
r_angle_refined_deg1.587
r_angle_other_deg1.136
r_chiral_restr0.097
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.007
r_gen_planes_other0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms30828
Nucleic Acid Atoms
Solvent Atoms702
Heterogen Atoms356

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling