1S1R

Crystal structures of prostaglandin D2 11-ketoreductase (AKR1C3) in complex with the non-steroidal anti-inflammatory drugs flufenamic acid and indomethacin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IHI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6291PEG, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.6353.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.917α = 90
b = 57.917β = 90
c = 206.168γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102001-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.93ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
125086.80.0921.710284502469121.3

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1IHI248.82337011841000.159630.157740.1962RANDOM13.693
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]
0.910.450.91-1.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.935
r_scangle_it2.635
r_scbond_it1.55
r_angle_refined_deg1.233
r_mcangle_it0.958
r_angle_other_deg0.797
r_mcbond_it0.497
r_symmetry_vdw_other0.255
r_nbd_other0.231
r_nbd_refined0.198
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.935
r_scangle_it2.635
r_scbond_it1.55
r_angle_refined_deg1.233
r_mcangle_it0.958
r_angle_other_deg0.797
r_mcbond_it0.497
r_symmetry_vdw_other0.255
r_nbd_other0.231
r_nbd_refined0.198
r_xyhbond_nbd_refined0.152
r_symmetry_vdw_refined0.152
r_symmetry_hbond_refined0.126
r_nbtor_other0.081
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2534
Nucleic Acid Atoms
Solvent Atoms302
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing