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Phosphotriesterase PTE_C23M_4
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 8 293 0.1M Tris pH=8
1M (NH4)2SO4
12% Glycerol
Crystal Properties Matthews coefficient Solvent content 3.17 61.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.93 α = 90 b = 69.93 β = 90 c = 185.81 γ = 90
Symmetry Space Group P 43 21 2
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++ 2015-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.541
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 1.665 22.96 98.44 0.02787 11.93 6.5 54190 18.76
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 1.665 1.724 96.59 0.2089 2.95 6.4
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 1.665 22.96 51507 2608 98.45 0.15958 0.15852 0.1727 0.18018 0.1883 RANDOM 19.205
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] 0.32 0.32 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.618 r_dihedral_angle_4_deg 16.458 r_dihedral_angle_3_deg 12.408 r_dihedral_angle_1_deg 6.361 r_long_range_B_refined 5.187 r_long_range_B_other 5.017 r_scangle_other 4.27 r_scbond_it 3.156 r_scbond_other 3.132 r_angle_refined_deg 2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.618 r_dihedral_angle_4_deg 16.458 r_dihedral_angle_3_deg 12.408 r_dihedral_angle_1_deg 6.361 r_long_range_B_refined 5.187 r_long_range_B_other 5.017 r_scangle_other 4.27 r_scbond_it 3.156 r_scbond_other 3.132 r_angle_refined_deg 2.42 r_mcangle_it 2.332 r_mcangle_other 2.332 r_mcbond_it 1.653 r_mcbond_other 1.652 r_angle_other_deg 1.298 r_chiral_restr 0.255 r_bond_refined_d 0.028 r_gen_planes_refined 0.014 r_bond_other_d 0.004 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 2477 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling PHASER phasing