5EZ4

2.11 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) P449M/Y450L double mutant from Staphylococcus aureus in complex with NAD+ and BME-modified 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 DROP7295Potein: 6 mg/ml, 10 mM Tris-HCl, pH 8.3, 500 mM NaCl, 5 mM BME, 5mM NAD+. Crystallization: Classics II D3: 100 mM HEPES, pH 7.0, 30%(v/v) Jeffamine ED-2001. Cryo: crystallization condition
Crystal Properties
Matthews coefficientSolvent content
2.9558.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 225.026α = 90
b = 102.158β = 104.85
c = 118.33γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-06-29MSINGLE 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
12.113099.90.1369.923.515407821.3
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)
12.112.1599.50.4962.063

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 4MPB2.1129.69141144747899.870.142810.141130.17474RANDOM22.98
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]
0.94-0.520.86-1.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.161
r_dihedral_angle_4_deg16.825
r_dihedral_angle_3_deg12.355
r_dihedral_angle_1_deg4.637
r_angle_refined_deg1.545
r_angle_other_deg1.008
r_chiral_restr0.098
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.161
r_dihedral_angle_4_deg16.825
r_dihedral_angle_3_deg12.355
r_dihedral_angle_1_deg4.637
r_angle_refined_deg1.545
r_angle_other_deg1.008
r_chiral_restr0.098
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.006
r_bond_other_d0.005
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15364
Nucleic Acid Atoms
Solvent Atoms2001
Heterogen Atoms305

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
ARPmodel building
PHASERphasing
Cootmodel building
BLU-MAXdata collection