4ZXU

2.85 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) H448F/P449M double mutant 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 DROP8.5295Crystallization: The Classics II Suite G5: 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 25% (w/v) PEG 3350. Protein: 5 mg/ml in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 0.5 mM TCEP, 5 mM NAD+. Cryo: crystallization condition
Crystal Properties
Matthews coefficientSolvent content
2.346.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.998α = 90
b = 168.999β = 104.51
c = 144.467γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2014-12-01MSINGLE 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
12.85301000.11711.93.89650764.4
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)
12.852.91000.68323.9

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 4mpb2.8529.8991344486499.850.166660.164220.21253RANDOM55.333
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]
-2.53-0.06-0.512.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.35
r_dihedral_angle_4_deg11.31
r_dihedral_angle_3_deg10.095
r_dihedral_angle_1_deg2.156
r_angle_refined_deg1.615
r_angle_other_deg1.098
r_chiral_restr0.097
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.35
r_dihedral_angle_4_deg11.31
r_dihedral_angle_3_deg10.095
r_dihedral_angle_1_deg2.156
r_angle_refined_deg1.615
r_angle_other_deg1.098
r_chiral_restr0.097
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.005
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 Atoms30833
Nucleic Acid Atoms
Solvent Atoms420
Heterogen Atoms427

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing