3RC1

Crystal Structure of KijD10, a 3-ketoreductase from Actinomadura kijaniata incomplex with NADP and TDP-benzene


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RBVmodel generated from 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
3.5164.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.826α = 90
b = 104.154β = 90
c = 145.283γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel mirrors2011-01-12MSINGLE 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
11.7184.6599.60.0810.0818.34.25961859618
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)
11.711.898.20.6430.6431.52.98171

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 from binary structure, PDB entry 3RBV1.71605660556605300899.610.205180.203670.23367RANDOM20.572
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]
-0.430.77-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.481
r_dihedral_angle_4_deg18.879
r_dihedral_angle_3_deg13.386
r_dihedral_angle_1_deg6.315
r_scangle_it6.231
r_scbond_it4.308
r_mcangle_it2.773
r_angle_refined_deg2.362
r_mcbond_it1.939
r_chiral_restr0.179
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.481
r_dihedral_angle_4_deg18.879
r_dihedral_angle_3_deg13.386
r_dihedral_angle_1_deg6.315
r_scangle_it6.231
r_scbond_it4.308
r_mcangle_it2.773
r_angle_refined_deg2.362
r_mcbond_it1.939
r_chiral_restr0.179
r_bond_refined_d0.01
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2568
Nucleic Acid Atoms
Solvent Atoms377
Heterogen Atoms91

Software

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