6AJB | pdb_00006ajb

Crystal structure of Trypanosoma brucei glycosomal isocitrate dehydrogenase in complex with NADH, alpha-ketoglutarate and ca2+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6AJ6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729320% PEG 6000, 100 mM HEPES/NaOH pH 7.0, 200mM NaCl
Crystal Properties
Matthews coefficientSolvent content
2.5451.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.52α = 90
b = 70.464β = 113.42
c = 121.929γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2016-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.90000SPring-8BL44XU

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
12.95093.80.0985.72.439505
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)
12.92.9589.20.6921.032.3

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6AJ62.919.9832695174181.90.196450.191780.190.283560.28RANDOM56.642
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]
0.060.25-0.540.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.404
r_dihedral_angle_3_deg22.193
r_dihedral_angle_4_deg20.418
r_dihedral_angle_1_deg8.52
r_long_range_B_other5.074
r_long_range_B_refined5.073
r_mcangle_it3.025
r_mcangle_other3.025
r_scangle_other2.876
r_angle_refined_deg1.898
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.404
r_dihedral_angle_3_deg22.193
r_dihedral_angle_4_deg20.418
r_dihedral_angle_1_deg8.52
r_long_range_B_other5.074
r_long_range_B_refined5.073
r_mcangle_it3.025
r_mcangle_other3.025
r_scangle_other2.876
r_angle_refined_deg1.898
r_mcbond_it1.761
r_mcbond_other1.761
r_scbond_it1.652
r_scbond_other1.652
r_angle_other_deg1.114
r_chiral_restr0.104
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13048
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms190

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing