2VCW

Complex structure of prostaglandin D2 synthase at 1.95A.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PD2PDB ENTRY 1PD2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.430% PEG6000, 1% DIOXANE, 5MM DTT, 5MM GSH, 0.05 M TRISHCL PH8.4
Crystal Properties
Matthews coefficientSolvent content
2.2846

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.858α = 90
b = 123.858β = 90
c = 106.62γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2003-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.958799.90.087.56.7585262.3
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)
11.952.0699.50.372.33.7

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 1PD21.9587.7155544296299.90.2080.2050.249RANDOM24.99
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]
0.360.36-0.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.245
r_dihedral_angle_4_deg12.917
r_dihedral_angle_3_deg10.866
r_dihedral_angle_1_deg2.773
r_scangle_it2.491
r_scbond_it1.628
r_angle_refined_deg1.276
r_mcangle_it1.232
r_mcbond_it0.773
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.245
r_dihedral_angle_4_deg12.917
r_dihedral_angle_3_deg10.866
r_dihedral_angle_1_deg2.773
r_scangle_it2.491
r_scbond_it1.628
r_angle_refined_deg1.276
r_mcangle_it1.232
r_mcbond_it0.773
r_nbtor_refined0.308
r_nbd_refined0.196
r_symmetry_vdw_refined0.149
r_symmetry_hbond_refined0.141
r_xyhbond_nbd_refined0.121
r_chiral_restr0.094
r_bond_refined_d0.01
r_gen_planes_refined0.005
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6326
Nucleic Acid Atoms
Solvent Atoms213
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing