1LWD

CRYSTAL STRUCTURE OF NADP-DEPENDENT ISOCITRATE DEHYDROGENASE FROM PORCINE HEART MITOCHONDRIA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherISOMORPHOUS SE-MET CRYSTAL STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.727720 MG/ML PROTEIN, 100 MM TRIETHANOLAMINE CHLORIDE PH 7.7, 150 MM SODIUM SULFATE, 8 MM ISOCITRATE, 4 MM MANGANESE SULFATE, 20% PEG 6000, 3% GLYCEROL, pH 7.70, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7355

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.86α = 90
b = 112.569β = 97
c = 66.08γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATERIGAKU RAXIS IVOSMIC MIRRORS1999-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
11.83095.90.07311.63.767886898868922.9
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)
1.81.8692.70.9631.43.6438584

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUTISOMORPHOUS SE-MET CRYSTAL STRUCTURE1.8529.238240077739772891.20.1980.1850.1820.21RANDOM27.4
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]
-1.2-0.26-1.012.21
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.6
c_scangle_it3.02
c_scbond_it2.03
c_mcangle_it1.74
c_angle_deg1.2
c_mcbond_it1.16
c_improper_angle_d0.76
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6570
Nucleic Acid Atoms
Solvent Atoms715
Heterogen Atoms38

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement