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Structure of a tryptophan synthase quinonoid intermediate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QOP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 293 50mM bicine (pH 7.8), 1mM EDTA, 5mM dithioerythritol, 0.02mM pyridoxal phosphate solution, 2mM spermine, and 10% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.53 51.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.024 α = 90 b = 58.908 β = 95.19 c = 67.086 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 210 double-crystal monochromator Si(111), beam focused by a toroidal mirror 2001-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 1.1 NSLS X12C
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 2.1 24 97.9 0.119 6.7 2.5 41128 41128 -3
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 2.1 2.2 98 0.348 3.1 2.5 5293
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 FOURIER SYNTHESIS THROUGHOUT 1QOP 2.1 23.7 39110 39110 2017 100 0.19997 0.19997 0.19798 0.2023 0.23843 0.2001 RANDOM 21.75
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] -2.21 -0.02 3.09 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.185 r_dihedral_angle_4_deg 15.804 r_dihedral_angle_3_deg 13.368 r_dihedral_angle_1_deg 5.526 r_scangle_it 2.014 r_scbond_it 1.189 r_angle_refined_deg 1.158 r_mcangle_it 0.734 r_mcbond_it 0.385 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.185 r_dihedral_angle_4_deg 15.804 r_dihedral_angle_3_deg 13.368 r_dihedral_angle_1_deg 5.526 r_scangle_it 2.014 r_scbond_it 1.189 r_angle_refined_deg 1.158 r_mcangle_it 0.734 r_mcbond_it 0.385 r_nbtor_refined 0.299 r_metal_ion_refined 0.222 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.169 r_symmetry_hbond_refined 0.145 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4936 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement ADSC data collection XDS data reduction XSCALE data scaling CNS phasing