3RC9

Crystal Structure of the K102A mutant of KijD10, a 3-ketoreductase from Actinomadura kijaniata in complex with TDP-benzene and NADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RBVmodel generated using binary complex, 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
3.5265.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.975α = 90
b = 104.464β = 90
c = 145.021γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel mirrors2011-01-22MSINGLE 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
11.9184.7691.10.0670.06712.94.13796237962
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)
11.912.0173.10.2540.2542.21.44673

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 complex, pdb entry 3RBV1.91723775237752201091.040.206270.204210.24525RANDOM21.192
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]
-0.350.82-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.878
r_dihedral_angle_4_deg21.129
r_dihedral_angle_3_deg14.492
r_dihedral_angle_1_deg6.894
r_scangle_it6.544
r_scbond_it4.492
r_mcangle_it2.675
r_angle_refined_deg2.337
r_mcbond_it1.834
r_chiral_restr0.167
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.878
r_dihedral_angle_4_deg21.129
r_dihedral_angle_3_deg14.492
r_dihedral_angle_1_deg6.894
r_scangle_it6.544
r_scbond_it4.492
r_mcangle_it2.675
r_angle_refined_deg2.337
r_mcbond_it1.834
r_chiral_restr0.167
r_bond_refined_d0.011
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2474
Nucleic Acid Atoms
Solvent Atoms199
Heterogen Atoms117

Software

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