3RBV

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOthermodel generated from MIR data

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82981.0 M sodium/potassium phosphate, 100 mM HEPPS, 10 mM NADP, 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 = 73.253α = 90
b = 104.032β = 90
c = 144.596γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel mirrors2011-01-10MSINGLE 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
11.984.4594.90.0830.0830.1124.34147941479
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)
11.9290.40.2840.2842.92.45420

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 MIR data1.9654147941479207894.950.193330.191490.22766RANDOM18.63
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]
0.170.33-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.813
r_dihedral_angle_4_deg21.14
r_dihedral_angle_3_deg14.716
r_dihedral_angle_1_deg6.932
r_scangle_it6.79
r_scbond_it4.593
r_mcangle_it2.734
r_angle_refined_deg2.269
r_mcbond_it1.858
r_chiral_restr0.167
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.813
r_dihedral_angle_4_deg21.14
r_dihedral_angle_3_deg14.716
r_dihedral_angle_1_deg6.932
r_scangle_it6.79
r_scbond_it4.593
r_mcangle_it2.734
r_angle_refined_deg2.269
r_mcbond_it1.858
r_chiral_restr0.167
r_bond_refined_d0.01
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2471
Nucleic Acid Atoms
Solvent Atoms287
Heterogen Atoms60

Software

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