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Structure of human prostaglandin D-synthase (hGSTS1-1) in complex with nocodazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CVD PDB ENTRY 2CVD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 25% (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 coefficient Solvent content 2.15 42.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.22 α = 90 b = 79.359 β = 90 c = 107.547 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 LN2 cooled first crystal, sagittal focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror, beam defining slits 2006-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97948 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.9 50 87.9 0.063 18.56 29738 28391 -1 -1 25.822
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 83.6 0.645 2.32 3.4 3056
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2CVD 1.91 37.97 -1 -1 29738 26912 1435 87.84 0.18587 0.18337 0.23195 0.2647 RANDOM 34.202
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 -0.26 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.285 r_dihedral_angle_3_deg 16.634 r_dihedral_angle_4_deg 15.718 r_dihedral_angle_1_deg 5.887 r_scangle_it 4.061 r_scbond_it 2.699 r_angle_refined_deg 1.779 r_mcangle_it 1.636 r_mcbond_it 1.097 r_symmetry_vdw_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.285 r_dihedral_angle_3_deg 16.634 r_dihedral_angle_4_deg 15.718 r_dihedral_angle_1_deg 5.887 r_scangle_it 4.061 r_scbond_it 2.699 r_angle_refined_deg 1.779 r_mcangle_it 1.636 r_mcbond_it 1.097 r_symmetry_vdw_refined 0.316 r_nbtor_refined 0.315 r_symmetry_hbond_refined 0.308 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.124 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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 Atoms Number Protein Atoms 3278 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 42
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling