4YWJ

Crystal structure of 4-hydroxy-tetrahydrodipicolinate reductase (HTPA reductase) from Pseudomonas aeruginosa


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ARZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5290Morpheus D9: 20mM of each: 1,6-Hexanediol; 1-Butanol, 1,2-Propanediol (racemic); 2-Propanol; 1,4-Butanediol; 1,3-Propanediol; 100mM Tris Base / Bicine pH 8.5, 30% each PEG 550MME, PEG 20000; PsaeA.00820.a.B1.PW37541 at 22.65 mg/ml; cryo: direct; tray 259740d90, puck hxm4-4
Crystal Properties
Matthews coefficientSolvent content
2.9158

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.01α = 90
b = 101.5β = 90
c = 144.51γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002014-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.978560APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.85099.40.0480.05318.11563326-324.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.851000.5170.5782.95.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1ARZ1.834.2871.3462927315399.10.16940.16770.2006Random selection36.7854
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.896
f_angle_d0.991
f_chiral_restr0.048
f_bond_d0.007
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3872
Nucleic Acid Atoms
Solvent Atoms356
Heterogen Atoms121

Software

Software
Software NamePurpose
XDSdata reduction
PHASERphasing
ARPmodel building
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling