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X-ray structure of Enterobacter cloaca transaldolase in complex with D-fructose-6-phosphate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S1V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 100 mM cacodylate buffer, pH 6.5, 10% (w/v) PEG3000, 10% (w/v) PEG 8000, 200 mM of MgCl2, 20 mM dihydroxtacetone, 20 mM, 20 mM D,L-glyceraldehyde-3-phosphate
Crystal Properties Matthews coefficient Solvent content 2.34 47.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.56 α = 90 b = 179.96 β = 90 c = 133.58 γ = 90
Symmetry Space Group C 2 2 21
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 RIGAKU RAXIS VII 2019-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.92 19.6 99.8 0.117 0.998 14.7 7.2 90439
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.97 0.912 0.771 2.3 7.2
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 3S1V 1.92 19.6 85902 4537 99.84 0.16762 0.16583 0.1776 0.20128 0.2114 RANDOM 20.293
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] 0.02 0.04 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.61 r_dihedral_angle_2_deg 11.557 r_dihedral_angle_1_deg 6.652 r_long_range_B_refined 6.282 r_long_range_B_other 6.254 r_scangle_other 5.039 r_scbond_it 3.4 r_scbond_other 3.387 r_mcangle_other 2.273 r_mcangle_it 2.272
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.61 r_dihedral_angle_2_deg 11.557 r_dihedral_angle_1_deg 6.652 r_long_range_B_refined 6.282 r_long_range_B_other 6.254 r_scangle_other 5.039 r_scbond_it 3.4 r_scbond_other 3.387 r_mcangle_other 2.273 r_mcangle_it 2.272 r_mcbond_it 1.661 r_mcbond_other 1.659 r_angle_refined_deg 1.119 r_angle_other_deg 0.435 r_chiral_restr 0.06 r_gen_planes_refined 0.01 r_bond_refined_d 0.004 r_gen_planes_other 0.001 r_bond_other_d r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8170 Nucleic Acid Atoms Solvent Atoms 661 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing