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Crystal structure of the aromatic prenyltransferase AtaPT (apo state) from Aspergillus terreus A8-4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I4Z
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 2.46 49.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.2 α = 90 b = 135.81 β = 90 c = 69.52 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 2013-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97 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 1.9 135.81 99.1 0.088 0.098 0.043 11.1 4.9 71707 71707
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 1.9 2 100 0.416 1.7 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 3I4Z 1.9 48.58 68155 3491 98.83 0.19384 0.19171 0.2013 0.23576 0.2429 RANDOM 30.338
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] -1.76 0.96 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.758 r_dihedral_angle_3_deg 15.08 r_dihedral_angle_4_deg 12.413 r_long_range_B_refined 7.28 r_long_range_B_other 7.259 r_dihedral_angle_1_deg 6.482 r_scangle_other 5.808 r_scbond_it 3.958 r_scbond_other 3.957 r_mcangle_other 3.855
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.758 r_dihedral_angle_3_deg 15.08 r_dihedral_angle_4_deg 12.413 r_long_range_B_refined 7.28 r_long_range_B_other 7.259 r_dihedral_angle_1_deg 6.482 r_scangle_other 5.808 r_scbond_it 3.958 r_scbond_other 3.957 r_mcangle_other 3.855 r_mcangle_it 3.854 r_mcbond_it 2.866 r_mcbond_other 2.863 r_angle_refined_deg 1.828 r_angle_other_deg 1.251 r_chiral_restr 0.119 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 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 6301 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOLREP phasing Coot model building SCALA data scaling MOSFLM data processing