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Crystal structure of the aromatic prenyltransferase AtaPT from Aspergillus terreus A8-4 in complex with dimethylallyl S-thiolodiphosphate
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 25 mM Bis-Tris, pH 6.0, 0.2 M (NH4)2SO4, 17% PEG 3350, 3.3% DDM
Crystal Properties Matthews coefficient Solvent content 2.37 48.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.29 α = 90 b = 132.97 β = 90 c = 68.48 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) 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 2.1 132.97 98.6 0.077 12.9 4.9 51286
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 2.1 2.21 93 0.356 2.1 4.2
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 2.1 132.97 48717 2530 98.37 0.19641 0.19453 0.2035 0.23313 0.2361 RANDOM 31.783
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] -0.1 0.22 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.616 r_dihedral_angle_4_deg 15.625 r_dihedral_angle_3_deg 14.312 r_long_range_B_other 6.955 r_long_range_B_refined 6.949 r_dihedral_angle_1_deg 6.729 r_scangle_other 5.597 r_scbond_it 3.728 r_scbond_other 3.728 r_mcangle_other 3.713
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.616 r_dihedral_angle_4_deg 15.625 r_dihedral_angle_3_deg 14.312 r_long_range_B_other 6.955 r_long_range_B_refined 6.949 r_dihedral_angle_1_deg 6.729 r_scangle_other 5.597 r_scbond_it 3.728 r_scbond_other 3.728 r_mcangle_other 3.713 r_mcangle_it 3.712 r_mcbond_it 2.708 r_mcbond_other 2.705 r_angle_refined_deg 1.832 r_angle_other_deg 1.366 r_chiral_restr 0.118 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d 0.007 r_gen_planes_other 0.006 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 6301 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOLREP phasing