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Crystal structure of the aromatic prenyltransferase AtaPT from Aspergillus terreus A8-4 in complex with dimethylallyl S-thiolodiphosphate and genistein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KCG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 289 0.1 M Bis-Tris pH 6.0, 0.2 M (NH4)2SO4, 17% PEG 3350, 3.3% DDM
Crystal Properties Matthews coefficient Solvent content 2.5 50.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.65 α = 90 b = 136.08 β = 90 c = 68.84 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 2014-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.99999 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 78.8 88.9 7 4.2 52312
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11
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 5KCG 2 78.8 52312 2731 88.62 0.19095 0.18848 0.2023 0.23772 0.2438 RANDOM 26.121
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] -0.68 0.94 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.593 r_dihedral_angle_4_deg 16.469 r_dihedral_angle_3_deg 15.802 r_dihedral_angle_1_deg 6.715 r_long_range_B_refined 6.203 r_long_range_B_other 6.137 r_scangle_other 4.657 r_scbond_it 3.059 r_scbond_other 3.059 r_mcangle_it 3.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.593 r_dihedral_angle_4_deg 16.469 r_dihedral_angle_3_deg 15.802 r_dihedral_angle_1_deg 6.715 r_long_range_B_refined 6.203 r_long_range_B_other 6.137 r_scangle_other 4.657 r_scbond_it 3.059 r_scbond_other 3.059 r_mcangle_it 3.056 r_mcangle_other 3.056 r_mcbond_it 2.148 r_mcbond_other 2.148 r_angle_refined_deg 1.884 r_angle_other_deg 1.062 r_chiral_restr 0.116 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 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 6311 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement MOLREP phasing Coot model building SCALA data scaling