2PH3

Crystal structure of 3-oxoacyl-[acyl carrier protein] reductase TTHA0415 from Thermus thermophilus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HQ1PDB entry 2HQ1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.52891.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (9.5 mg/ml) AND SOLUTION CONTAINING 0.1 M Tris-HCl pH 8.5, 2.4 M di-Ammonium Phosphate, VAPOR DIFFUSION, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2144.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.525α = 90
b = 76.525β = 90
c = 137.562γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDROSENBAUM2007-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM0.97240APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.915099.90.06522.820.835274
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)
11.911.981000.14418.93504

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 REPLACEMENTTHROUGHOUTPDB entry 2HQ11.9119.673519835198176399.960.1910.1910.1890.229RANDOM17.961
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]
0.010.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.993
r_dihedral_angle_4_deg17.75
r_dihedral_angle_3_deg14.816
r_dihedral_angle_1_deg5.65
r_scangle_it4.247
r_scbond_it2.714
r_mcangle_it1.545
r_angle_refined_deg1.516
r_mcbond_it1.434
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.993
r_dihedral_angle_4_deg17.75
r_dihedral_angle_3_deg14.816
r_dihedral_angle_1_deg5.65
r_scangle_it4.247
r_scbond_it2.714
r_mcangle_it1.545
r_angle_refined_deg1.516
r_mcbond_it1.434
r_nbtor_refined0.302
r_symmetry_hbond_refined0.298
r_xyhbond_nbd_refined0.281
r_symmetry_vdw_refined0.243
r_nbd_refined0.233
r_chiral_restr0.11
r_bond_refined_d0.017
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3621
Nucleic Acid Atoms
Solvent Atoms188
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
HKL-2000data reduction
SGXPROphasing