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Complex structure of prostaglandin D2 synthase at 1.95A.
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 30% PEG6000, 1% DIOXANE, 5MM DTT, 5MM GSH, 0.05 M TRISHCL PH8.4
Crystal Properties Matthews coefficient Solvent content 2.28 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.858 α = 90 b = 123.858 β = 90 c = 106.62 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 2003-11-27 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 1.95 87 99.9 0.08 7.5 6.7 58526 2.3
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 1.95 2.06 99.5 0.37 2.3 3.7
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PD2 1.95 87.71 55544 2962 99.9 0.208 0.205 0.249 RANDOM 24.99
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] 0.36 0.36 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.245 r_dihedral_angle_4_deg 12.917 r_dihedral_angle_3_deg 10.866 r_dihedral_angle_1_deg 2.773 r_scangle_it 2.491 r_scbond_it 1.628 r_angle_refined_deg 1.276 r_mcangle_it 1.232 r_mcbond_it 0.773 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.245 r_dihedral_angle_4_deg 12.917 r_dihedral_angle_3_deg 10.866 r_dihedral_angle_1_deg 2.773 r_scangle_it 2.491 r_scbond_it 1.628 r_angle_refined_deg 1.276 r_mcangle_it 1.232 r_mcbond_it 0.773 r_nbtor_refined 0.308 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.149 r_symmetry_hbond_refined 0.141 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.094 r_bond_refined_d 0.01 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_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 Atoms Number Protein Atoms 6326 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing