4K02

Crystal structure of AtDHNAT1, a 1,4-dihydroxy-2-naphthoyl-CoA thioesterase from Arabidopsis thaliana


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SC0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72982.7 M NaHCOOH, 100 mM Tris-HCl, 10 mM n-octyl- D-glucoside in protein, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5752.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.529α = 90
b = 99.529β = 90
c = 61.257γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARMOSAIC 300 mm CCD2012-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.033APS23-ID-D

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
11.928.8896.40.05848.835.32698426984
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)
11.91.9584.10.7642.422.5

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1SC01.928.882670226702136195.650.184510.184510.183180.21055RANDOM63.246
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]
-1.2-1.2-1.23.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.344
r_dihedral_angle_4_deg22.782
r_dihedral_angle_3_deg16.24
r_dihedral_angle_1_deg8.583
r_angle_refined_deg1.618
r_angle_other_deg0.842
r_chiral_restr0.108
r_gen_planes_refined0.011
r_bond_refined_d0.008
r_gen_planes_other0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.344
r_dihedral_angle_4_deg22.782
r_dihedral_angle_3_deg16.24
r_dihedral_angle_1_deg8.583
r_angle_refined_deg1.618
r_angle_other_deg0.842
r_chiral_restr0.108
r_gen_planes_refined0.011
r_bond_refined_d0.008
r_gen_planes_other0.005
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1914
Nucleic Acid Atoms
Solvent Atoms52
Heterogen Atoms

Software

Software
Software NamePurpose
JBluIce-EPICSdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling