4XDZ

Holo structure of ketol-acid reductoisomerase from Ignisphaera aggregans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4KQX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62950.1 M bis-tris pH 6, 22% polyethylene glycol monomethylether 5000
Crystal Properties
Matthews coefficientSolvent content
2.3146.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.579α = 90
b = 90.753β = 100.25
c = 69.525γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.9795SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.1568.415950.0790.0960.0546.93236179
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.151.2182.40.870.870.6430.92.528356

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 REPLACEMENTTHROUGHOUT4KQX1.1568.4152243411121594.870.15820.15650.1895RANDOM13.086
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]
-0.23-0.010.10.13
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free24.013
r_rigid_bond_restr7.914
r_sphericity_bonded7.468
r_angle_refined_deg2.461
r_mcangle_it1.86
r_mcbond_it1.565
r_mcbond_other1.561
r_angle_other_deg1.034
r_chiral_restr0.287
r_bond_refined_d0.024
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free24.013
r_rigid_bond_restr7.914
r_sphericity_bonded7.468
r_angle_refined_deg2.461
r_mcangle_it1.86
r_mcbond_it1.565
r_mcbond_other1.561
r_angle_other_deg1.034
r_chiral_restr0.287
r_bond_refined_d0.024
r_gen_planes_refined0.016
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5139
Nucleic Acid Atoms
Solvent Atoms596
Heterogen Atoms178

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
PHASERphasing