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Crystal structure of the dihydroxyacetone kinase from E. coli in complex with glyceraldehyde
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 pH 5.00
Crystal Properties Matthews coefficient Solvent content 2.55 51.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.54 α = 90 b = 97.315 β = 90 c = 85.997 γ = 90
Symmetry Space Group P 21 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 25 99.3 0.074 16.1 3.5 54971 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2 19.65 53425 1544 100 0.179 0.178 0.2063 0.231 RANDOM 17.07
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] -1.16 2.23 -1.07
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.391 r_scbond_it 4.538 r_mcangle_it 3.844 r_dihedral_angle_1_deg 3.815 r_mcbond_it 2.809 r_angle_refined_deg 1.731 r_nbd_refined 0.231 r_symmetry_vdw_refined 0.215 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.168
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.391 r_scbond_it 4.538 r_mcangle_it 3.844 r_dihedral_angle_1_deg 3.815 r_mcbond_it 2.809 r_angle_refined_deg 1.731 r_nbd_refined 0.231 r_symmetry_vdw_refined 0.215 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.168 r_chiral_restr 0.15 r_bond_refined_d 0.017 r_gen_planes_refined 0.001 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5070 Nucleic Acid Atoms Solvent Atoms 478 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement