☰ Navigation Tabs
Crystal structure of tetrameric biodegradative threonine deaminase (TdcB) from Salmonella typhimurium in complex with CMP at 2.5A resolution (Hexagonal form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GN0 BIODEGRADATIVE THREONINE DEAMINASE FROM SALMONELLA TYPHIMURIUM (PDB CODE 1GN0)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 0.1 M Citrate, 25% PEG4000, 10% Hexanediol , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.49 64.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.145 α = 90 b = 161.145 β = 90 c = 68.723 γ = 120
Symmetry Space Group P 6 2 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 IMAGE PLATE MAC Science DIP-2030 Osmic mirror 2006-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.93 SPring-8 BL44XU
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 2.5 30 99.8 0.055 53.4 39.32 18675 18675 66
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 2.5 2.59 100 0.383 7.56 1820
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 (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 BIODEGRADATIVE THREONINE DEAMINASE FROM SALMONELLA TYPHIMURIUM (PDB
CODE 1GN0) 2.5 30 17629 17629 951 99.63 0.19823 0.1967 0.199 0.2259 0.2258 RANDOM 62.336
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] -1.06 -0.53 -1.06 1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.105 r_dihedral_angle_4_deg 18.223 r_dihedral_angle_3_deg 14.165 r_dihedral_angle_1_deg 5.36 r_scangle_it 1.509 r_angle_refined_deg 1.062 r_scbond_it 0.883 r_angle_other_deg 0.717 r_mcangle_it 0.53 r_symmetry_vdw_refined 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.105 r_dihedral_angle_4_deg 18.223 r_dihedral_angle_3_deg 14.165 r_dihedral_angle_1_deg 5.36 r_scangle_it 1.509 r_angle_refined_deg 1.062 r_scbond_it 0.883 r_angle_other_deg 0.717 r_mcangle_it 0.53 r_symmetry_vdw_refined 0.28 r_mcbond_it 0.272 r_nbd_refined 0.198 r_nbtor_refined 0.168 r_nbd_other 0.163 r_xyhbond_nbd_refined 0.141 r_symmetry_vdw_other 0.126 r_symmetry_hbond_refined 0.106 r_metal_ion_refined 0.096 r_nbtor_other 0.08 r_symmetry_metal_ion_refined 0.064 r_chiral_restr 0.057 r_mcbond_other 0.05 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2432 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing