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Crystal structure of the dimethylallyl tryptophan synthase FgaPT2 from Aspergillus fumigatus in complex with Trp and DMSPP
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 7 277 26% 1,3-butanediol, 50mM sodium L-lactate, 100mM sodium MOPSO pH 7.0, 2mM DTT, vapour diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.28 46.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.07 α = 90 b = 97.85 β = 90 c = 125.19 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MARMOSAIC 225 mm CCD 2009-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.275 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.08 24.94 99.9 0.1 17.7 5.9 59038 58992 3 37.7
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 2.08 2.13 99.9 0.495 3.44 58992
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 R free PDB ENTRY 3I4Z 2.1 24.94 3.44 55615 55615 1663 100 0.15 0.151 0.149 0.1686 0.2 0.2157 RANDOM 32.424
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] 1.91 -0.97 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.056 r_dihedral_angle_4_deg 18.034 r_dihedral_angle_3_deg 14.945 r_dihedral_angle_1_deg 6.197 r_scangle_it 3.117 r_mcangle_it 2.552 r_scbond_it 2.257 r_mcbond_it 1.699 r_angle_refined_deg 1.553 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.056 r_dihedral_angle_4_deg 18.034 r_dihedral_angle_3_deg 14.945 r_dihedral_angle_1_deg 6.197 r_scangle_it 3.117 r_mcangle_it 2.552 r_scbond_it 2.257 r_mcbond_it 1.699 r_angle_refined_deg 1.553 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6871 Nucleic Acid Atoms Solvent Atoms 585 Heterogen Atoms 70
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction REFMAC phasing