3GUG

Crystal structure of AKR1C1 L308V mutant in complex with NADP and 3,5-dichlorosalicylic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3C3UPDB ENTRY 3C3U

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52950.1M MES, 25% Polyethylene glycol monomethyl ether 550, 0.01M Zinc sulphate heptahydrate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.243.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.412α = 90
b = 83.885β = 90.98
c = 48.914γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMirrors2008-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54179

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
11.93094.60.04811.74.01240302273312
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)
1.91.9794.10.362.74.812237

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUTPDB ENTRY 3C3U1.929.03112403022522121694.620.193920.190410.26021RANDOM27.165
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]
-1.46-1.112.31-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.935
r_dihedral_angle_4_deg18.002
r_dihedral_angle_3_deg14.168
r_dihedral_angle_1_deg11.133
r_scangle_it3.561
r_scbond_it2.587
r_angle_refined_deg2.023
r_mcangle_it1.472
r_mcbond_it1.057
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.935
r_dihedral_angle_4_deg18.002
r_dihedral_angle_3_deg14.168
r_dihedral_angle_1_deg11.133
r_scangle_it3.561
r_scbond_it2.587
r_angle_refined_deg2.023
r_mcangle_it1.472
r_mcbond_it1.057
r_nbtor_refined0.304
r_xyhbond_nbd_refined0.269
r_symmetry_vdw_refined0.224
r_nbd_refined0.2
r_symmetry_hbond_refined0.19
r_chiral_restr0.161
r_metal_ion_refined0.141
r_bond_refined_d0.022
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2559
Nucleic Acid Atoms
Solvent Atoms318
Heterogen Atoms61

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling