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Crystal structure of Transaldolase (EC 2.2.1.2) (TM0295) from Thermotoga maritima at 2.40 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L6W PDB entry 1L6W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 7 293 30.0% 1,2-propanediol, 0.2M (NH4)2SO4, 10.0% Glycerol, 0.1M HEPES, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.75 54.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.298 α = 90 b = 104.419 β = 108.99 c = 171.124 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 CCD ADSC 2004-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.4 104.19 85.9 0.07 9.1 2.5 162044 59
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 56.1 0.581 1.3 2.1 7812
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 (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 1L6W 2.4 83.13 153845 8140 85.87 0.19884 0.19632 0.2041 0.24694 0.2506 RANDOM 47.997
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] -1.2 -0.29 1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.791 r_dihedral_angle_4_deg 21.676 r_dihedral_angle_3_deg 19.614 r_scangle_it 7.925 r_dihedral_angle_1_deg 5.994 r_scbond_it 5.626 r_mcangle_it 2.374 r_angle_refined_deg 1.508 r_mcbond_it 1.399 r_angle_other_deg 0.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.791 r_dihedral_angle_4_deg 21.676 r_dihedral_angle_3_deg 19.614 r_scangle_it 7.925 r_dihedral_angle_1_deg 5.994 r_scbond_it 5.626 r_mcangle_it 2.374 r_angle_refined_deg 1.508 r_mcbond_it 1.399 r_angle_other_deg 0.933 r_mcbond_other 0.228 r_xyhbond_nbd_refined 0.214 r_symmetry_hbond_refined 0.21 r_nbd_refined 0.205 r_xyhbond_nbd_other 0.188 r_nbtor_refined 0.179 r_nbd_other 0.175 r_symmetry_vdw_other 0.169 r_symmetry_vdw_refined 0.132 r_chiral_restr 0.098 r_nbtor_other 0.09 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 31669 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 131
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement CCP4 data scaling