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Crystal structure of the aromatic prenyltransferase AtaPT from Aspergillus terreus A8-4 in complex with geranyl S-thiolodiphosphate and (+)-butyrolactone II
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 289 25 mM Bis-Tris, 0.2 M (NH4)2SO4, 17% PEG3350, 3.3% DDM
Crystal Properties Matthews coefficient Solvent content 2.43 49.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.95 α = 90 b = 134.91 β = 90 c = 68.69 γ = 90
Symmetry Space Group P 21 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 CCD ADSC QUANTUM 315r 2013-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97907 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.3 134.91 97 0.083 0.096 0.047 10 3.7 39454 39454
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 2.3 2.42 93.2 0.288 2.6 3.2
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 2.3 56.371 37460 1950 96.59 0.20604 0.20399 0.2074 0.2456 0.2484 RANDOM 39.09
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] 0.01 1.16 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.348 r_dihedral_angle_3_deg 16.305 r_dihedral_angle_4_deg 12.761 r_long_range_B_other 8.117 r_long_range_B_refined 8.115 r_dihedral_angle_1_deg 6.384 r_scangle_other 6.228 r_mcangle_it 5.05 r_mcangle_other 5.049 r_scbond_it 3.927
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.348 r_dihedral_angle_3_deg 16.305 r_dihedral_angle_4_deg 12.761 r_long_range_B_other 8.117 r_long_range_B_refined 8.115 r_dihedral_angle_1_deg 6.384 r_scangle_other 6.228 r_mcangle_it 5.05 r_mcangle_other 5.049 r_scbond_it 3.927 r_scbond_other 3.927 r_mcbond_other 3.336 r_mcbond_it 3.335 r_angle_refined_deg 1.843 r_angle_other_deg 1.372 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 6082 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOLREP phasing