1S1P

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6291PEG, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2244.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.681α = 90
b = 63.119β = 90
c = 96.113γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-11-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.93ESRFID14-1

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
11.252.798.50.05916.451066311050329.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.21.2690.10.2424.12.613800

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.23899571523298.510.146790.14630.15594RANDOM13.5
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]
0.150.17-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.496
r_dihedral_angle_1_deg4.449
r_scangle_it2.243
r_sphericity_free1.438
r_scbond_it1.407
r_angle_refined_deg1.346
r_mcangle_it1.043
r_sphericity_bonded0.955
r_angle_other_deg0.834
r_rigid_bond_restr0.726
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.496
r_dihedral_angle_1_deg4.449
r_scangle_it2.243
r_sphericity_free1.438
r_scbond_it1.407
r_angle_refined_deg1.346
r_mcangle_it1.043
r_sphericity_bonded0.955
r_angle_other_deg0.834
r_rigid_bond_restr0.726
r_mcbond_it0.584
r_symmetry_vdw_refined0.345
r_symmetry_vdw_other0.341
r_symmetry_hbond_refined0.245
r_nbd_refined0.237
r_nbd_other0.196
r_xyhbond_nbd_refined0.159
r_chiral_restr0.079
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2582
Nucleic Acid Atoms
Solvent Atoms440
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing