☰ Navigation Tabs
Crystal structure of 5-dimethylallyl tryptophan synthase from Streptomyces coelicolor in complex with DMASPP and Trp
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
20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.82 32.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.658 α = 90 b = 70.147 β = 92.722 c = 91.082 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 1.696 45.5 97 0.065 0.99 15.4 4.5 62994 32.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.696 1.8 1 0.59
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 1.696 45.49 60392 1812 96.948 0.182 0.1811 0.1899 0.2189 0.2236 28.515
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] -0.008 -0.269 0.396 -0.361
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.805 r_dihedral_angle_4_deg 20.921 r_dihedral_angle_3_deg 14.104 r_dihedral_angle_1_deg 6.585 r_lrange_it 5.228 r_lrange_other 5.134 r_scangle_it 2.48 r_scangle_other 2.479 r_mcangle_it 2.155 r_mcangle_other 2.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.805 r_dihedral_angle_4_deg 20.921 r_dihedral_angle_3_deg 14.104 r_dihedral_angle_1_deg 6.585 r_lrange_it 5.228 r_lrange_other 5.134 r_scangle_it 2.48 r_scangle_other 2.479 r_mcangle_it 2.155 r_mcangle_other 2.155 r_scbond_it 1.544 r_scbond_other 1.543 r_chiral_restr_other 1.463 r_angle_refined_deg 1.455 r_angle_other_deg 1.34 r_mcbond_it 1.275 r_mcbond_other 1.275 r_nbd_other 0.217 r_nbd_refined 0.199 r_symmetry_xyhbond_nbd_refined 0.196 r_symmetry_nbd_other 0.188 r_symmetry_nbd_refined 0.179 r_xyhbond_nbd_refined 0.166 r_nbtor_refined 0.158 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.068 r_symmetry_xyhbond_nbd_other 0.061 r_xyhbond_nbd_other 0.03 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5269 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing