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The impact of molecular variants, crystallization conditions and space group on structure-ligand complexes: A case study on Bacterial Phosphotriesterase Variants and complexes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8P7F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.5M (NH4)2SO4
17% Glycerol
0.1M Tris pH=7.0
Crystal Properties Matthews coefficient Solvent content 3.15 60.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.56 α = 90 b = 69.56 β = 90 c = 186.64 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++ 2014-05-22 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) Rpim I (All) CC (Half) 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 1.77 34.8 99.92 0.02413 0.999 18.97 20 45349
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.87 0.0978 0.974 6.41
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.77 34.8 43061 2285 99.9 0.158 0.157 0.1604 0.186 0.1879 RANDOM 17.59
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] 0.33 0.33 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.232 r_dihedral_angle_4_deg 17.677 r_dihedral_angle_3_deg 11.566 r_dihedral_angle_1_deg 7.188 r_long_range_B_refined 5.412 r_long_range_B_other 5.135 r_scangle_other 4.076 r_scbond_it 2.882 r_scbond_other 2.795 r_mcangle_other 2.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.232 r_dihedral_angle_4_deg 17.677 r_dihedral_angle_3_deg 11.566 r_dihedral_angle_1_deg 7.188 r_long_range_B_refined 5.412 r_long_range_B_other 5.135 r_scangle_other 4.076 r_scbond_it 2.882 r_scbond_other 2.795 r_mcangle_other 2.185 r_mcangle_it 2.179 r_angle_refined_deg 1.992 r_angle_other_deg 1.691 r_mcbond_it 1.53 r_mcbond_other 1.53 r_chiral_restr 0.169 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.001 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 2490 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling PHASER phasing