3H7U

Crystal structure of the plant stress-response enzyme AKR4C9


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S1PPDB entry 1S1P

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6291400 mM Ammonium acetate, 100 mM Tri-sodium citrate dihydrate, 37.5% w/v PEG 4000, pH 6.0, VAPOR DIFFUSION, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.5251.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.355α = 90
b = 70.687β = 107.22
c = 65.767γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.933ESRFID14-1

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
11.2523.48920.04316.13.9957668799011.7

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 REPLACEMENTTHROUGHOUTPDB entry 1S1P1.2523.4883557443091.90.132450.131210.15619RANDOM12.05
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]
0.01-0.04-0.040.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.634
r_dihedral_angle_3_deg11.131
r_dihedral_angle_4_deg6.678
r_dihedral_angle_1_deg5.708
r_sphericity_free5.298
r_scangle_it3.347
r_sphericity_bonded2.423
r_scbond_it2.281
r_mcangle_it1.618
r_angle_refined_deg1.457
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.634
r_dihedral_angle_3_deg11.131
r_dihedral_angle_4_deg6.678
r_dihedral_angle_1_deg5.708
r_sphericity_free5.298
r_scangle_it3.347
r_sphericity_bonded2.423
r_scbond_it2.281
r_mcangle_it1.618
r_angle_refined_deg1.457
r_rigid_bond_restr1.025
r_mcbond_it1.024
r_angle_other_deg0.888
r_mcbond_other0.454
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2511
Nucleic Acid Atoms
Solvent Atoms530
Heterogen Atoms52

Software

Software
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling