3BV7

Crystal structure of Delta(4)-3-ketosteroid 5-beta-reductase in complex with NADP and glycerol. Resolution: 1.79 A.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BUR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5277Protein: 5.0 mg/mL AKR1D1, 2.0 mM NADPH, 2.0 mM 5-beta-cholestan-3-one, 10.0 mM Tris (pH 7.4). Precipitant buffer: 0.1 M Tris (pH 7.0), 10-20% (wt/vol) PEG 4000, 10% isopropanol., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3647.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.826α = 90
b = 109.833β = 90
c = 129.186γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDRosenbaum-Rock monochromator high-resolution double-crystal Si (111) sagittal focusing. Rosenbaum-Rock vertical focusing mirror.2007-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.00APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.795098.60.10920.54.16677466774
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.791.851000.373.44.16684

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESIS3BUR1.7950633206332028000.23610.23610.2571RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
s_non_zero_chiral_vol0.031
s_from_restr_planes0.024
s_bond_d0.02
s_angle_d0.012
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5254
Nucleic Acid Atoms
Solvent Atoms348
Heterogen Atoms114

Software

Software
Software NamePurpose
SHELXL-97refinement
CNSrefinement
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing