3ZBN

Crystal structure of SCP2 thiolase from Leishmania mexicana. Complex of the C123A mutant with Coenzyme A.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZBGPDB ENTRY 3ZBG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18100 MM TRIS PH 8.0, 200 MM NACL AND 20 % PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.346.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.26α = 90
b = 89.83β = 105.8
c = 126.24γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135HELIOS MIRRORS2012-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

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
12.4572.299.80.1510.26.262765
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)
12.452.5599.20.352.63.1

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 3ZBG2.45121.4759546319599.730.2110.208680.2541RANDOM16.565
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]
-0.70.450.610.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.78
r_dihedral_angle_4_deg17.292
r_dihedral_angle_3_deg15.501
r_dihedral_angle_1_deg6.16
r_angle_refined_deg1.565
r_angle_other_deg1.35
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.78
r_dihedral_angle_4_deg17.292
r_dihedral_angle_3_deg15.501
r_dihedral_angle_1_deg6.16
r_angle_refined_deg1.565
r_angle_other_deg1.35
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.007
r_gen_planes_other0.006
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 Atoms12896
Nucleic Acid Atoms
Solvent Atoms373
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing