4QJE

1.85 Angstrom resolution crystal structure of apo betaine aldehyde dehydrogenase (betB) G234S mutant from Staphylococcus aureus (IDP00699) with BME-free sulfinic acid form of Cys289


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4NI4PDB ENTRY 4NI4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82957 mg/mL protein in 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 0.5 mM TCEP, crystallization conditions: PACT Suite (C5): 0.1 M PCB buffer, pH 8.0, 25% w/v PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.8556.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 218.665α = 90
b = 102.929β = 101.42
c = 118.074γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDberyllium lenses2014-04-17MSINGLE 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)R Sym 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
11.853099.90.0990.09915.923.8217702217702-317.6
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)
11.851.8899.60.6342.33.610794

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 4NI41.8529.832067672067671093499.70.1510.149710.17537RANDOM21.14
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]
1.90.070.13-1.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.403
r_dihedral_angle_4_deg17.439
r_dihedral_angle_3_deg12.094
r_dihedral_angle_1_deg4.375
r_angle_refined_deg1.537
r_angle_other_deg1.089
r_chiral_restr0.098
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.403
r_dihedral_angle_4_deg17.439
r_dihedral_angle_3_deg12.094
r_dihedral_angle_1_deg4.375
r_angle_refined_deg1.537
r_angle_other_deg1.089
r_chiral_restr0.098
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15344
Nucleic Acid Atoms
Solvent Atoms2472
Heterogen Atoms107

Software

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