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Complex structure of prostaglandin D2 synthase at 2.25A.
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 8.4 PEG 6000 30%, TCEP 5MM, GSH 5MM, DIOXANE 1%, MGCL2 5MM, TRISHCL (PH8.4) 50 MM
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.521 α = 90 b = 123.521 β = 90 c = 106.289 γ = 90
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 CCD MIRRORS 2004-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.25 87 98.5 0.12 6.6 3.4 37285 1.7
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 2.25 2.31 97.5 0.52 1.7 3.3
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PD2 2.25 50 34207 1811 95.1 0.188 0.184 0.1877 0.255 RANDOM 25.05
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] 0.48 0.48 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.454 r_dihedral_angle_4_deg 13.949 r_dihedral_angle_3_deg 12.536 r_dihedral_angle_1_deg 2.995 r_scangle_it 2.422 r_scbond_it 1.6 r_angle_refined_deg 1.467 r_mcangle_it 1.246 r_mcbond_it 0.745 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.454 r_dihedral_angle_4_deg 13.949 r_dihedral_angle_3_deg 12.536 r_dihedral_angle_1_deg 2.995 r_scangle_it 2.422 r_scbond_it 1.6 r_angle_refined_deg 1.467 r_mcangle_it 1.246 r_mcbond_it 0.745 r_nbtor_refined 0.31 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.17 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.109 r_metal_ion_refined 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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_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 Atoms Number Protein Atoms 6418 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing