5Y9Z

Crystal structure of rat hematopoietic prostaglandin D synthase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PD2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIQUID DIFFUSION8.529350 mM Tris-HCl, pH 8.5, 35% PEG6000, 5 mM DTT, 5mM GSH, 2 mM Dioxane, 2 mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.2745.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.54α = 90
b = 79.84β = 90
c = 96.6γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-01-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.8SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.0948.399.60.0390.0420.014112.57.7175007
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.091.1199.50.5290.5680.2010.9297.2

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 REPLACEMENTTHROUGHOUT1PD21.0948.3166098878299.50.15670.15550.1786RANDOM12.662
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]
0.52-0.08-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.88
r_sphericity_free21.73
r_dihedral_angle_4_deg12.846
r_dihedral_angle_3_deg11.254
r_sphericity_bonded6.965
r_dihedral_angle_1_deg5.305
r_rigid_bond_restr1.937
r_angle_refined_deg1.416
r_angle_other_deg0.937
r_chiral_restr0.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.88
r_sphericity_free21.73
r_dihedral_angle_4_deg12.846
r_dihedral_angle_3_deg11.254
r_sphericity_bonded6.965
r_dihedral_angle_1_deg5.305
r_rigid_bond_restr1.937
r_angle_refined_deg1.416
r_angle_other_deg0.937
r_chiral_restr0.088
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3280
Nucleic Acid Atoms
Solvent Atoms523
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata collection
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction