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X-ray structure of Enterobacter cloaca transaldolase
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
Crystal Properties Matthews coefficient Solvent content 2.36 47.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99 α = 90 b = 180.07 β = 90 c = 134.04 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 PIXEL DECTRIS PILATUS 6M 2019-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 1.63 46.68 99.9 0.068 0.999 17.6 6.5 148396
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 1.63 1.67 0.913 0.736 2.1
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 1.63 46.48 140948 7448 99.9 0.17451 0.17331 0.1848 0.19735 0.2042 RANDOM 19.368
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] -0.13 0.12 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.537 r_dihedral_angle_2_deg 8.728 r_dihedral_angle_1_deg 6.241 r_long_range_B_refined 5.482 r_long_range_B_other 5.446 r_scangle_other 4.809 r_scbond_it 3.333 r_scbond_other 3.333 r_mcangle_other 2.162 r_mcangle_it 2.161
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.537 r_dihedral_angle_2_deg 8.728 r_dihedral_angle_1_deg 6.241 r_long_range_B_refined 5.482 r_long_range_B_other 5.446 r_scangle_other 4.809 r_scbond_it 3.333 r_scbond_other 3.333 r_mcangle_other 2.162 r_mcangle_it 2.161 r_mcbond_it 1.624 r_mcbond_other 1.624 r_angle_refined_deg 1.203 r_angle_other_deg 0.438 r_chiral_restr 0.065 r_gen_planes_refined 0.011 r_bond_refined_d 0.005 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 8095 Nucleic Acid Atoms Solvent Atoms 830 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing