3C3U

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MRQPDB ENTRY 1MRQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52950.1M MES, 25% Polyglycol monomethylether 550, 0.01M Zinc sulphate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2144.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.364α = 90
b = 84.236β = 91.26
c = 49.183γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMirrors2007-12-13MSINGLE 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
11.83096.30.050411.52.99273402632912
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)
1.81.8687.60.22992.52.72076

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 1MRQ1.830112734026329131696.220.176720.174460.21761RANDOM23.654
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]
-0.53-0.590.92-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.992
r_dihedral_angle_4_deg14.979
r_dihedral_angle_3_deg12.028
r_dihedral_angle_1_deg11.616
r_scangle_it3.361
r_scbond_it2.325
r_angle_refined_deg1.564
r_mcangle_it1.378
r_mcbond_it0.973
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.992
r_dihedral_angle_4_deg14.979
r_dihedral_angle_3_deg12.028
r_dihedral_angle_1_deg11.616
r_scangle_it3.361
r_scbond_it2.325
r_angle_refined_deg1.564
r_mcangle_it1.378
r_mcbond_it0.973
r_nbtor_refined0.306
r_symmetry_vdw_refined0.224
r_nbd_refined0.199
r_xyhbond_nbd_refined0.177
r_symmetry_hbond_refined0.14
r_chiral_restr0.113
r_metal_ion_refined0.056
r_bond_refined_d0.017
r_symmetry_metal_ion_refined0.008
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2592
Nucleic Acid Atoms
Solvent Atoms328
Heterogen Atoms61

Software

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