4NEA

1.90 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) from Staphylococcus aureus 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 DROP8.32957 mg/mL protein in 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 0.5 mM TCEP, 2 mM NAD+, crystallization condition: JCSG+ Suite #G9 (0.1 M potassium thiocyonate, 30% w/v PEG2000 MME), VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.1943.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.728α = 90
b = 142.073β = 90
c = 163.112γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDberyllium lenses2013-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
11.93097.90.08222.77.2155760155760-324.4
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)
11.91.931000.4464.67.27884

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 4MPB1.929.85147576147576778197.850.142040.139650.188RANDOM26.568
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]
-0.331.27-0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.951
r_dihedral_angle_4_deg17.605
r_dihedral_angle_3_deg14.349
r_dihedral_angle_1_deg6.327
r_angle_refined_deg1.698
r_angle_other_deg0.85
r_chiral_restr0.1
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.951
r_dihedral_angle_4_deg17.605
r_dihedral_angle_3_deg14.349
r_dihedral_angle_1_deg6.327
r_angle_refined_deg1.698
r_angle_other_deg0.85
r_chiral_restr0.1
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15543
Nucleic Acid Atoms
Solvent Atoms1989
Heterogen Atoms192

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling