4AOV | pdb_00004aov

DpIDH-NADP. The complex structures of Isocitrate dehydrogenase from Clostridium thermocellum and Desulfotalea psychrophila, support a new active site locking mechanism


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROPHANGING DROP METHOD. RESERVOIR SOLUTIONS WITH 100 MM TRIS/HCL BUFFER AT PH 7.4, 1.7-1.9 M AMMONIUM SULFATE, 2% PEG 400 AND 60 MM MAGNESIUM SULFATE. PROTEIN SOLUTION: 20 MG/ML DPIDH, 10 MM NADP AND 10 MM DL-ISOCITRATE.
Crystal Properties
Matthews coefficientSolvent content
2.3347.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.64α = 90
b = 98.91β = 103.94
c = 71.89γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM1AESRFBM1A

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
11.934098.10.0910.73.83084417.9
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)
11.932.0398.10.412.73.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.932029252156398.130.177450.17490.180.225420.23RANDOM19.858
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]
0.320.520.05-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.956
r_dihedral_angle_4_deg17.199
r_dihedral_angle_3_deg14.282
r_dihedral_angle_1_deg6.189
r_scangle_it2.495
r_scbond_it1.715
r_angle_refined_deg1.406
r_mcangle_it1.09
r_mcbond_it0.7
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.956
r_dihedral_angle_4_deg17.199
r_dihedral_angle_3_deg14.282
r_dihedral_angle_1_deg6.189
r_scangle_it2.495
r_scbond_it1.715
r_angle_refined_deg1.406
r_mcangle_it1.09
r_mcbond_it0.7
r_nbtor_refined0.302
r_symmetry_vdw_refined0.223
r_nbd_refined0.203
r_symmetry_hbond_refined0.161
r_xyhbond_nbd_refined0.149
r_chiral_restr0.099
r_bond_refined_d0.012
r_gen_planes_refined0.005
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 Atoms3180
Nucleic Acid Atoms
Solvent Atoms227
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement