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Crystal structure of the brevianamide F prenyltransferase FtmPT1 from Aspergillus fumigatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I4Z PDB ENTRY 3I4Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 1.3M ammonium sulfate, 0.2M lithium sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.94 36.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.85 α = 90 b = 82.85 β = 90 c = 121.76 γ = 90
Symmetry Space Group P 41 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 MARMOSAIC 225 mm CCD 2009-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 30 96.4 0.072 0.102 13.79 9.3 15277 14721 3 3 47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.57 100 0.254 0.32 5.48 9.8 1091
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 3I4Z 2.5 20 3 14690 13957 733 96.45 0.219 0.189 0.18642 0.1863 0.2365 0.2303 RANDOM 51.092
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] -3.61 -3.61 7.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.881 r_dihedral_angle_4_deg 18.092 r_dihedral_angle_3_deg 16.589 r_dihedral_angle_1_deg 5.793 r_scangle_it 3.335 r_mcangle_it 2.724 r_scbond_it 2.347 r_mcbond_it 1.77 r_angle_refined_deg 1.155 r_angle_other_deg 0.844
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.881 r_dihedral_angle_4_deg 18.092 r_dihedral_angle_3_deg 16.589 r_dihedral_angle_1_deg 5.793 r_scangle_it 3.335 r_mcangle_it 2.724 r_scbond_it 2.347 r_mcbond_it 1.77 r_angle_refined_deg 1.155 r_angle_other_deg 0.844 r_mcbond_other 0.588 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3419 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 21
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling