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Crystal structure of 5-dimethylallyltryptophan synthase from Streptomyces coelicolor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5INJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 150 mM Bis-tris
23% PEG3350
Crystal Properties Matthews coefficient Solvent content 1.85 33.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.88 α = 90 b = 70.454 β = 92.946 c = 91.145 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M-F 2020-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00002 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.5 45.5 97.7 0.01 0.99 15.4 4.6 88635 27.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.59 0.61 1.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5INJ 1.5 41.055 88630 1773 97.692 0.19 0.1891 0.1986 0.2199 0.2293 23.913
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] 0.064 0.016 0.478 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.075 r_dihedral_angle_4_deg 17.52 r_dihedral_angle_3_deg 13.789 r_dihedral_angle_1_deg 6.543 r_lrange_it 5.215 r_lrange_other 5.151 r_scangle_it 1.877 r_scangle_other 1.876 r_mcangle_it 1.747 r_mcangle_other 1.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.075 r_dihedral_angle_4_deg 17.52 r_dihedral_angle_3_deg 13.789 r_dihedral_angle_1_deg 6.543 r_lrange_it 5.215 r_lrange_other 5.151 r_scangle_it 1.877 r_scangle_other 1.876 r_mcangle_it 1.747 r_mcangle_other 1.747 r_angle_refined_deg 1.425 r_angle_other_deg 1.385 r_scbond_it 1.119 r_scbond_other 1.119 r_mcbond_it 1.005 r_mcbond_other 1.005 r_symmetry_nbd_refined 0.314 r_nbd_other 0.249 r_nbd_refined 0.206 r_symmetry_xyhbond_nbd_refined 0.195 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_other 0.088 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5227 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing