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Structure of the prostaglandin D synthase from the parasitic nematode Onchocerca volvulus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PD2 PDB Entry: 1PD2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 Reservoir: 22% PEG4000, 10% Isopropanol, 0.1M Hepes pH 7.5
Protein stock: 5.5mg/ml in 100mM Na-acetate-trihydrate pH 8.0, temperature 298K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.38 48.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.783 α = 90 b = 90.995 β = 90 c = 106.01 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 2004-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.803 EMBL/DESY, HAMBURG X13
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 2 50 99.7 0.069 15.1 34249
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 2 2.03 99 0.36 1700
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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: 1PD2 2 50 33856 1711 99.73 0.184 0.184 0.181 0.234 0.2389 RANDOM 19.275
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] -0.45 0.92 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.628 r_scangle_it 4.537 r_scbond_it 2.802 r_mcangle_it 1.836 r_angle_refined_deg 1.716 r_angle_other_deg 1.081 r_mcbond_it 0.991 r_symmetry_vdw_refined 0.258 r_symmetry_vdw_other 0.255 r_nbd_other 0.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.628 r_scangle_it 4.537 r_scbond_it 2.802 r_mcangle_it 1.836 r_angle_refined_deg 1.716 r_angle_other_deg 1.081 r_mcbond_it 0.991 r_symmetry_vdw_refined 0.258 r_symmetry_vdw_other 0.255 r_nbd_other 0.248 r_chiral_restr 0.221 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.194 r_xyhbond_nbd_refined 0.15 r_nbtor_other 0.089 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3267 Nucleic Acid Atoms Solvent Atoms 415 Heterogen Atoms 40
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction