3DOP

Crystal structure of 5beta-reductase (AKR1D1) in complex with NADP+ and 5beta-dihydrotestosterone, Resolution 2.00A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CMFPDB ENTRY 3CMF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7277ISOPROPANOL, PEG 4000, TRIS-HCL, PH 7.0, 10.0mM 5bDHT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2344.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.872α = 90
b = 109.495β = 90
c = 129.199γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray186IMAGE PLATERIGAKU RAXIS IV++2008-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
1227.8497.20.1187.64.7473444734417.1
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)
22.0797.40.4131

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 3CMF227.8447218203596.90.220.220.257RANDOM21.1
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]
2.35-1.37-0.98
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.8
c_scangle_it2.69
c_scbond_it1.94
c_mcangle_it1.86
c_mcbond_it1.25
c_angle_deg1.2
c_improper_angle_d0.86
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5254
Nucleic Acid Atoms
Solvent Atoms588
Heterogen Atoms117

Software

Software
Software NamePurpose
CNSrefinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing