4Q92

1.90 Angstrom resolution crystal structure of apo betaine aldehyde dehydrogenase (betB) G234S mutant from Staphylococcus aureus (IDP00699) with BME-modified 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 DROP82957.3 mg/mL protein in 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 5 mM BME against PACT Suite A5/5 (0.1 M SPG, pH 8.0, 25% w/v PEG1500), VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2344.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 157.363α = 90
b = 156.438β = 110.01
c = 88.417γ = 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
11.93098.80.1040.10417.33.9155391155391-321
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)
11.91.9397.90.5852.43.97680

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 4NI41.929.5147596147596779598.730.19510.19360.2229RANDOM24.801
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]
2.22-0.1-2.580.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.991
r_dihedral_angle_4_deg16.119
r_dihedral_angle_3_deg12.525
r_dihedral_angle_1_deg4.47
r_angle_refined_deg1.513
r_angle_other_deg1.108
r_chiral_restr0.096
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.991
r_dihedral_angle_4_deg16.119
r_dihedral_angle_3_deg12.525
r_dihedral_angle_1_deg4.47
r_angle_refined_deg1.513
r_angle_other_deg1.108
r_chiral_restr0.096
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15456
Nucleic Acid Atoms
Solvent Atoms1591
Heterogen Atoms20

Software

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