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Crystal structure of the aromatic prenyltransferase AtaPT from Aspergillus terreus A8-4 in complex with geranyl 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 2.43 49.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.33 α = 90 b = 135.67 β = 90 c = 68.61 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 2 135.67 91.3 0.106 0.119 0.053 9.9 4.3 55640 55640
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 2.11 85.8 0.308 2.2 4.5
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 48.24 52816 2793 90.42 0.18776 0.18586 0.1942 0.22356 0.2301 RANDOM 23.118
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] -0.44 0.54 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.094 r_dihedral_angle_3_deg 14.605 r_dihedral_angle_4_deg 14.44 r_dihedral_angle_1_deg 6.076 r_long_range_B_refined 6.051 r_long_range_B_other 6.034 r_scangle_other 4.821 r_scbond_it 3.206 r_scbond_other 3.206 r_mcangle_it 2.831
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.094 r_dihedral_angle_3_deg 14.605 r_dihedral_angle_4_deg 14.44 r_dihedral_angle_1_deg 6.076 r_long_range_B_refined 6.051 r_long_range_B_other 6.034 r_scangle_other 4.821 r_scbond_it 3.206 r_scbond_other 3.206 r_mcangle_it 2.831 r_mcangle_other 2.831 r_mcbond_it 2.023 r_mcbond_other 2.022 r_angle_refined_deg 1.911 r_angle_other_deg 1.323 r_chiral_restr 0.117 r_bond_refined_d 0.024 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 330 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOLREP phasing