3VL4

3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at 410 MPa


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293PEG 3350, calcium chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.550.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.61α = 90
b = 57.633β = 118.98
c = 75.504γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDADSC QUANTUM 210r2011-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A0.700Photon FactoryAR-NW12A

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
11.885086.40.07210.52.827609
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)
11.881.9191.50.3982.71469

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 3VKZ1.8848.6327584138386.210.15880.1560.2129RANDOM18.6019
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]
0.180.150.23-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.152
r_dihedral_angle_4_deg21.901
r_dihedral_angle_3_deg16.309
r_dihedral_angle_1_deg6.288
r_scangle_it6.185
r_scbond_it3.83
r_mcangle_it2.342
r_angle_refined_deg2.008
r_mcbond_it1.331
r_chiral_restr0.156
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.152
r_dihedral_angle_4_deg21.901
r_dihedral_angle_3_deg16.309
r_dihedral_angle_1_deg6.288
r_scangle_it6.185
r_scbond_it3.83
r_mcangle_it2.342
r_angle_refined_deg2.008
r_mcbond_it1.331
r_chiral_restr0.156
r_bond_refined_d0.024
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2759
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms14

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing