3RCB

Crystal structure of the K102E 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 DROP82981.2 M sodium/potassium phosphate, 100 mM HEPPS, 5 mM TDP-benzene, 5 mM NADP, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.4664.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.371α = 90
b = 103.497β = 90
c = 145.154γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel mirrors2011-01-26MSINGLE 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
12.4984.2796.90.0960.09610.641897018970
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)
12.492.5886.90.2380.2383.210.61756

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 3RBV2.4965180101801095997.040.191920.188830.25299RANDOM17.118
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]
-0.390.180.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.872
r_dihedral_angle_4_deg20.421
r_dihedral_angle_3_deg15.376
r_dihedral_angle_1_deg6.79
r_scangle_it5.637
r_scbond_it3.755
r_angle_refined_deg2.275
r_mcangle_it2.13
r_mcbond_it1.166
r_chiral_restr0.135
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.872
r_dihedral_angle_4_deg20.421
r_dihedral_angle_3_deg15.376
r_dihedral_angle_1_deg6.79
r_scangle_it5.637
r_scbond_it3.755
r_angle_refined_deg2.275
r_mcangle_it2.13
r_mcbond_it1.166
r_chiral_restr0.135
r_bond_refined_d0.01
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2478
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms117

Software

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