4XDY

Structure of NADH-preferring ketol-acid reductoisomerase from an uncultured archean


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52950.1 M bis-tris pH 5, 20% w/v polyethylene glycol 1500
Crystal Properties
Matthews coefficientSolvent content
3.5164.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.695α = 90
b = 141.748β = 90
c = 148.598γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-03-30MSINGLE 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)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
11.535102.5799.40.0887.24.5157419
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)
11.5351.799.80.9631.54.5

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 REPLACEMENTTHROUGHOUT4KQX1.535102.57145320769997.250.180220.178750.20914RANDOM25.89
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]
-1.070.20.87
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined6.041
r_long_range_B_other6.041
r_scangle_other5.349
r_scbond_it3.663
r_scbond_other3.663
r_mcangle_other2.924
r_mcangle_it2.92
r_mcbond_it2.246
r_mcbond_other2.245
r_angle_refined_deg2.038
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined6.041
r_long_range_B_other6.041
r_scangle_other5.349
r_scbond_it3.663
r_scbond_other3.663
r_mcangle_other2.924
r_mcangle_it2.92
r_mcbond_it2.246
r_mcbond_other2.245
r_angle_refined_deg2.038
r_angle_other_deg0.95
r_chiral_restr0.128
r_bond_refined_d0.022
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5144
Nucleic Acid Atoms
Solvent Atoms359
Heterogen Atoms126

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing