3PPI

Crystal structure of 3-hydroxyacyl-CoA dehydrogenase type-2 from Mycobacterium avium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SO81SO8 modified with CCP4 program chainsaw

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9290MD PACT screen, condition b6: 100mM MIB buffer pH 9.0, 25% PEG 1500; MYAVA.00554.A.A1 PS00625 AT 44.4MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.9558

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.81α = 90
b = 161.15β = 90
c = 65.57γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.31.0000ALS5.0.3

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
125099.80.0918.697.28588085726-326.1
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)
122.051000.4914.57.36287

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1SO8 modified with CCP4 program chainsaw2508588085496427599.60.1460.1450.171RANDOM15.88
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]
1.27-0.87-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.787
r_dihedral_angle_3_deg12.256
r_dihedral_angle_4_deg11.86
r_dihedral_angle_1_deg5.906
r_scangle_it3.058
r_scbond_it1.867
r_angle_refined_deg1.276
r_mcangle_it1.204
r_angle_other_deg0.905
r_mcbond_it0.668
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.787
r_dihedral_angle_3_deg12.256
r_dihedral_angle_4_deg11.86
r_dihedral_angle_1_deg5.906
r_scangle_it3.058
r_scbond_it1.867
r_angle_refined_deg1.276
r_mcangle_it1.204
r_angle_other_deg0.905
r_mcbond_it0.668
r_mcbond_other0.152
r_chiral_restr0.076
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7242
Nucleic Acid Atoms
Solvent Atoms883
Heterogen Atoms26

Software

Software
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling