3EE2 | pdb_00003ee2

Structure of human prostaglandin D-synthase (hGSTS1-1) in complex with nocodazole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CVDPDB ENTRY 2CVD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529825% (w/v) PEG 6000, 25mM MgCL2, 100mM Tris-HCl pH 7.5, 1% (w/v) dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1542.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.22α = 90
b = 79.359β = 90
c = 107.547γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315LN2 cooled first crystal, sagittal focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror, beam defining slits2006-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97948APS19-ID

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
11.95087.90.06318.562973828391-1-125.822
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)
11.91.9783.60.6452.323.43056

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2CVD1.9137.97-1-12973826912143587.840.185870.183370.180.231950.23RANDOM34.202
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]
-0.2-0.260.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.285
r_dihedral_angle_3_deg16.634
r_dihedral_angle_4_deg15.718
r_dihedral_angle_1_deg5.887
r_scangle_it4.061
r_scbond_it2.699
r_angle_refined_deg1.779
r_mcangle_it1.636
r_mcbond_it1.097
r_symmetry_vdw_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.285
r_dihedral_angle_3_deg16.634
r_dihedral_angle_4_deg15.718
r_dihedral_angle_1_deg5.887
r_scangle_it4.061
r_scbond_it2.699
r_angle_refined_deg1.779
r_mcangle_it1.636
r_mcbond_it1.097
r_symmetry_vdw_refined0.316
r_nbtor_refined0.315
r_symmetry_hbond_refined0.308
r_nbd_refined0.216
r_xyhbond_nbd_refined0.182
r_chiral_restr0.124
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3278
Nucleic Acid Atoms
Solvent Atoms180
Heterogen Atoms42

Software

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