4QTO

1.65 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) from Staphylococcus aureus with BME-modified Cys289 and PEG molecule in active site


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3.52957 mg/mL protein in 10 mM betaine (not observed in structure), 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 5 mM BME, crystallization: The Classics II Suite D4 (40): 0.1 M citric acid, pH 3.5, 25% w/v PEG3350, cryoprotectant: well solution, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.8656.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 224.249α = 90
b = 102.474β = 104.45
c = 118.178γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDberyllium lenses2014-06-16MSINGLE 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
11.653098.60.08216.74.3307248307248-317
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)
11.651.6897.50.6312.54.315078

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 4MPB1.6529.712903622903621543398.570.136890.13590.15554RANDOM18.754
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]
0.62-0.34-0.05-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.811
r_dihedral_angle_4_deg16.054
r_dihedral_angle_3_deg10.897
r_dihedral_angle_1_deg4.084
r_angle_refined_deg1.643
r_angle_other_deg1.14
r_chiral_restr0.11
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.811
r_dihedral_angle_4_deg16.054
r_dihedral_angle_3_deg10.897
r_dihedral_angle_1_deg4.084
r_angle_refined_deg1.643
r_angle_other_deg1.14
r_chiral_restr0.11
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.006
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15398
Nucleic Acid Atoms
Solvent Atoms2663
Heterogen Atoms129

Software

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