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X-ray structure of WT PTE with ethyl phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OB3 PDB entry 2OB3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M Bis-Tris, 20% polyethylene glycol monomethyl ether 5000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.06 40.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.286 α = 104.73 b = 45.338 β = 93.4 c = 78.913 γ = 97.65
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 180 IMAGE PLATE RIGAKU RAXIS IV mirrors 2007-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.83 50 100 0.08 0.061 13.2 2.9 47158 47158
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.83 1.9 100 0.344 0.319 3 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2OB3 1.83 20.49 44744 44744 2413 93.6 0.1431 0.14031 0.1407 0.19557 0.1971 RANDOM 15.991
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] 0.56 0.04 -0.31 -0.41 -0.27 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.027 r_dihedral_angle_4_deg 18.263 r_dihedral_angle_3_deg 13.045 r_dihedral_angle_1_deg 5.953 r_scangle_it 2.175 r_mcangle_it 1.558 r_angle_refined_deg 1.419 r_scbond_it 1.395 r_mcbond_it 1.006 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.027 r_dihedral_angle_4_deg 18.263 r_dihedral_angle_3_deg 13.045 r_dihedral_angle_1_deg 5.953 r_scangle_it 2.175 r_mcangle_it 1.558 r_angle_refined_deg 1.419 r_scbond_it 1.395 r_mcbond_it 1.006 r_nbtor_refined 0.302 r_nbd_refined 0.198 r_symmetry_hbond_refined 0.157 r_symmetry_vdw_refined 0.149 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.11 r_metal_ion_refined 0.077 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5116 Nucleic Acid Atoms Solvent Atoms 843 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing