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Phosphotriesterase PTE_C23_2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HYZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.05M HEPES pH=7.5
13% Polyacrylic acid 5100 Na
0.01M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.18 43.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.66 α = 90 b = 81.16 β = 94.83 c = 70.66 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2014-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5415
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 70.41 99.96 0.05192 11.84 6.1 44881 18.32
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 2.02 100 0.248 3.18
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1HYZ 1.95 70.41 42615 2264 99.98 0.15849 0.15636 0.1672 0.19871 0.2071 RANDOM 18.565
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] 0.88 0.43 0.18 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.208 r_dihedral_angle_4_deg 17.607 r_dihedral_angle_3_deg 13.026 r_dihedral_angle_1_deg 6.52 r_long_range_B_refined 4.656 r_long_range_B_other 4.623 r_scangle_other 3.515 r_scbond_it 2.265 r_scbond_other 2.257 r_mcangle_other 1.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.208 r_dihedral_angle_4_deg 17.607 r_dihedral_angle_3_deg 13.026 r_dihedral_angle_1_deg 6.52 r_long_range_B_refined 4.656 r_long_range_B_other 4.623 r_scangle_other 3.515 r_scbond_it 2.265 r_scbond_other 2.257 r_mcangle_other 1.955 r_mcangle_it 1.952 r_angle_refined_deg 1.865 r_mcbond_it 1.362 r_mcbond_other 1.362 r_angle_other_deg 1.229 r_chiral_restr 0.11 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4977 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction SCALA data scaling PHASER phasing