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Crystal structure of Toluene 2,3-Dioxygenase Reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D7Y pdb entry: 1D7Y including all side chains
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.7 286 0.1 M Tris pH 8.5, 1.5 M (NH)4SO 2 and 12% (v/v) glycerol, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Crystal Properties Matthews coefficient Solvent content 2.71 54.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.128 α = 90 b = 77.128 β = 90 c = 156.372 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 ADSC QUANTUM 210 2004-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 1.0332 NSLS X6A
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 1.8 19.86 99 0.076 9.24 44352 1 1
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 1.8 1.86 96.4 0.386 4 7.04 4216
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 MOLECULAR REPLACEMENT THROUGHOUT pdb entry: 1D7Y including all side chains 1.8 20 44198 44198 2229 99.28 0.205 0.205 0.203 0.2008 0.243 0.2397 RANDOM 28.002
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] 1.09 1.09 -2.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.31 r_dihedral_angle_4_deg 17.776 r_dihedral_angle_3_deg 13.779 r_dihedral_angle_1_deg 5.622 r_scangle_it 3.389 r_scbond_it 2.071 r_angle_refined_deg 1.521 r_mcangle_it 1.299 r_mcbond_it 0.86 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.31 r_dihedral_angle_4_deg 17.776 r_dihedral_angle_3_deg 13.779 r_dihedral_angle_1_deg 5.622 r_scangle_it 3.389 r_scbond_it 2.071 r_angle_refined_deg 1.521 r_mcangle_it 1.299 r_mcbond_it 0.86 r_nbtor_refined 0.297 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.195 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2940 Nucleic Acid Atoms Solvent Atoms 465 Heterogen Atoms 105
Software Software Software Name Purpose d*TREK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection d*TREK data reduction