3ZBK

Crystal structure of SCP2 thiolase from Leishmania mexicana: The C123A mutant.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5100 MM MES PH6.5, 10% MME PEG 5000, 10% DMSO, 10% MPD
Crystal Properties
Matthews coefficientSolvent content
3.160.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.266α = 90
b = 123.266β = 90
c = 132.936γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135HELIOS MIRRORS2012-07-21MSINGLE 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
11.961.699.80.214.615.589877
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)
11.921000.634.110.9

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 3ZBG1.9106.7585194451299.630.222440.220530.25888RANDOM17.445
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]
0.510.260.51-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.787
r_dihedral_angle_4_deg14.888
r_dihedral_angle_3_deg14.673
r_dihedral_angle_1_deg6.589
r_angle_refined_deg1.827
r_angle_other_deg1.38
r_chiral_restr0.116
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.787
r_dihedral_angle_4_deg14.888
r_dihedral_angle_3_deg14.673
r_dihedral_angle_1_deg6.589
r_angle_refined_deg1.827
r_angle_other_deg1.38
r_chiral_restr0.116
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.006
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 Atoms6448
Nucleic Acid Atoms
Solvent Atoms649
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing