3RC2

Crystal Structure of KijD10, a 3-ketoreductase from Actinomadura kijaniata in complex with TDP-benzene and NADP; open conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RBVmodel generated using binary structure, pdb entry 3RBV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82981.0 M sodium/potassium phosphate, 100 mM HEPPS, 5 mM NADP, 5 mM TDP-benzene, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.5265.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.087α = 90
b = 104.822β = 90
c = 144.469γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel mirrors2011-01-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.884.8495.20.0840.08413.154931449314
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.989.30.5270.5272.92.36888

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTmodel generated using binary structure, pdb entry 3RBV1.8604680646806250895.20.208720.206890.2428RANDOM19.808
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]
-1.230.910.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.998
r_dihedral_angle_4_deg22.389
r_dihedral_angle_3_deg14.685
r_scangle_it6.739
r_dihedral_angle_1_deg6.703
r_scbond_it4.662
r_mcangle_it2.935
r_angle_refined_deg2.293
r_mcbond_it2.02
r_chiral_restr0.169
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.998
r_dihedral_angle_4_deg22.389
r_dihedral_angle_3_deg14.685
r_scangle_it6.739
r_dihedral_angle_1_deg6.703
r_scbond_it4.662
r_mcangle_it2.935
r_angle_refined_deg2.293
r_mcbond_it2.02
r_chiral_restr0.169
r_bond_refined_d0.01
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2489
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms91

Software

Software
Software NamePurpose
PROTEUM PLUSdata collection
PHASERphasing
REFMACrefinement
SAINTdata reduction
SADABSdata scaling