3KLJ

Crystal structure of NADH:rubredoxin oxidoreductase from Clostridium acetobutylicum


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529335% (v/v) PEG 400, 0.1M Tris-HCl pH 8.5, 0.15M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5451.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.576α = 90
b = 98.576β = 90
c = 88.267γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDADSC QUANTUM 3152008-11-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0000SPring-8BL41XU

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
12.12099.90.05211.74.2259832598338.3
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)
12.12.211000.4423.24.24806

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.12024627131999.850.21570.213660.25435RANDOM19.958
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]
-0.1-0.10.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.303
r_dihedral_angle_4_deg18.859
r_dihedral_angle_3_deg17.859
r_dihedral_angle_1_deg6.453
r_scangle_it2.114
r_scbond_it1.323
r_angle_refined_deg1.196
r_mcangle_it0.853
r_mcbond_it0.46
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.303
r_dihedral_angle_4_deg18.859
r_dihedral_angle_3_deg17.859
r_dihedral_angle_1_deg6.453
r_scangle_it2.114
r_scbond_it1.323
r_angle_refined_deg1.196
r_mcangle_it0.853
r_mcbond_it0.46
r_chiral_restr0.086
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2890
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms53

Software

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