2ZTW | pdb_00002ztw

Structure of 3-isopropylmalate dehydrogenase in complex with the inhibitor and NAD+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HEXPDB ENTRY 1HEX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.22934M sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH7.2
Crystal Properties
Matthews coefficientSolvent content
3.9168.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.507α = 90
b = 103.507β = 90
c = 186.418γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21SPring-8BL26B2

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
12.7989.899.30.1216.615425
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)
2.792.9990.495

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1HEX2.7925.881455176699.310.199880.197290.20.249650.25RANDOM33.649
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]
-0.1-0.05-0.10.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.116
r_dihedral_angle_4_deg22.989
r_dihedral_angle_3_deg20.127
r_dihedral_angle_1_deg6.039
r_scangle_it3.946
r_scbond_it2.232
r_angle_refined_deg1.653
r_mcangle_it1.321
r_mcbond_it0.67
r_chiral_restr0.099
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2595
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms36

Software

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