2UXR

Complex with isocitrate and the protein isocitrate dehydrogenase from the psychrophilic bacterium Desulfotalea psychrophila


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2UXQPDB ENTRY 2UXQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.4100 MM TRIS/HCL BUFFER PH 7.4, 1.7-1.9 M AMMONIUM SULPHATE, 2% PEG 400, 6 0 MM MGSO4
Crystal Properties
Matthews coefficientSolvent content
2.753.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.56α = 90
b = 121.74β = 90
c = 273.77γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12.3501000.1212.55.74411130.2
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)
12.32.421000.4745.8

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 2UXQ2.32041756221899.90.1990.1950.259RANDOM31.54
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]
0.270.23-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.118
r_dihedral_angle_4_deg19.813
r_dihedral_angle_3_deg18.256
r_dihedral_angle_1_deg7.464
r_scangle_it3.627
r_scbond_it2.438
r_angle_refined_deg1.815
r_mcangle_it1.555
r_mcbond_it0.954
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.118
r_dihedral_angle_4_deg19.813
r_dihedral_angle_3_deg18.256
r_dihedral_angle_1_deg7.464
r_scangle_it3.627
r_scbond_it2.438
r_angle_refined_deg1.815
r_mcangle_it1.555
r_mcbond_it0.954
r_nbtor_refined0.306
r_symmetry_vdw_refined0.234
r_nbd_refined0.226
r_xyhbond_nbd_refined0.186
r_chiral_restr0.117
r_symmetry_hbond_refined0.092
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms6345
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing