3INM

Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase R132H mutant in complex with NADPH, ALPHA-KETOGLUTARATE and CALCIUM(2+)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1T0LPDB ENTRY 1T0L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293Protein component: 8 mg/ml IDH, 20mM Tris-HCl pH 7.5, 100mM sodium chloride, 10mM NADPH, 10mM calcium chloride, 75mM alpha-ketoglutaric acid sodium salt. Precipitant: 100mM MES pH 6.5, 20% PEG 6000. Ratio of protein component to precipitant in initial hanging drop: 2:1., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6753.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.12α = 90
b = 274.69β = 90
c = 116.5γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMIRROR AND MONOCHROMETER2009-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.0809NSLSX29A

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
12.12592.40.0820.38.6899588312131
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)
12.12.1858.80.3052.42.15232

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1T0L2.124.918310978956415392.360.2220.220.262RANDOM33.273
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]
0.03-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.825
r_dihedral_angle_4_deg25.226
r_dihedral_angle_3_deg19.723
r_dihedral_angle_1_deg6.858
r_scangle_it3.774
r_scbond_it2.321
r_mcangle_it1.318
r_angle_refined_deg1.105
r_mcbond_it0.698
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.825
r_dihedral_angle_4_deg25.226
r_dihedral_angle_3_deg19.723
r_dihedral_angle_1_deg6.858
r_scangle_it3.774
r_scbond_it2.321
r_mcangle_it1.318
r_angle_refined_deg1.105
r_mcbond_it0.698
r_chiral_restr0.09
r_bond_refined_d0.014
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9706
Nucleic Acid Atoms
Solvent Atoms301
Heterogen Atoms198

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection