6AJ6

Crystal structure of Trypanosoma brucei glycosomal isocitrate dehydrogenase in complex with NADP+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1T0L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.629320% PEG 3350, 200mM potassium nitrate
Crystal Properties
Matthews coefficientSolvent content
2.3848.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.442α = 90
b = 109.754β = 89.98
c = 64.961γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2015-12-12MSINGLE 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
13.25098.40.0996.63.314385
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)
13.23.2699.20.7991.453.2

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 REPLACEMENTTHROUGHOUT1T0L3.245.021158255883.880.216490.212190.30858RANDOM79.105
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]
20.9226.33-17.14-3.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.716
r_dihedral_angle_3_deg22.999
r_dihedral_angle_4_deg16.827
r_long_range_B_refined11.723
r_long_range_B_other11.722
r_dihedral_angle_1_deg10.41
r_mcangle_it7.735
r_mcangle_other7.734
r_scangle_other6.317
r_mcbond_it4.593
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.716
r_dihedral_angle_3_deg22.999
r_dihedral_angle_4_deg16.827
r_long_range_B_refined11.723
r_long_range_B_other11.722
r_dihedral_angle_1_deg10.41
r_mcangle_it7.735
r_mcangle_other7.734
r_scangle_other6.317
r_mcbond_it4.593
r_mcbond_other4.592
r_scbond_it3.682
r_scbond_other3.682
r_angle_refined_deg1.875
r_angle_other_deg1.138
r_chiral_restr0.097
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.003
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 Atoms6564
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms96

Software

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