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1.25 Angstrom Resolution Crystal Structure of 4-hydroxythreonine-4-phosphate Dehydrogenase from Klebsiella pneumoniae.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HI1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 292 Protein: 6.9 mg/ml, 0.01M Tris-HCl pH 8.3;
Screen: Classics II (G2), 0.2M Lithium sulfate, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350;
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.355 α = 90 b = 76.216 β = 106.78 c = 92.113 γ = 90
Symmetry Space Group C 1 2 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 MARMOSAIC 300 mm CCD C(111) 2018-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.25 30 99.8 0.053 0.053 0.06 0.028 24.6 4.3 177342 -3 12.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 97.7 0.549 0.549 0.654 0.349 0.8 2.3 3.3
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 2HI1 1.25 29.67 168266 8941 99.77 0.11509 0.11384 0.1143 0.1392 0.1393 RANDOM 16.874
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] 0.33 0.01 0.24 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.359 r_sphericity_free 19.899 r_dihedral_angle_4_deg 13.475 r_dihedral_angle_3_deg 11.275 r_rigid_bond_restr 8.784 r_sphericity_bonded 6.937 r_dihedral_angle_1_deg 4.679 r_long_range_B_refined 3.057 r_long_range_B_other 2.545 r_scangle_other 1.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.359 r_sphericity_free 19.899 r_dihedral_angle_4_deg 13.475 r_dihedral_angle_3_deg 11.275 r_rigid_bond_restr 8.784 r_sphericity_bonded 6.937 r_dihedral_angle_1_deg 4.679 r_long_range_B_refined 3.057 r_long_range_B_other 2.545 r_scangle_other 1.981 r_scbond_it 1.685 r_scbond_other 1.613 r_mcangle_it 1.458 r_mcangle_other 1.457 r_angle_refined_deg 1.283 r_mcbond_it 1.261 r_mcbond_other 1.261 r_angle_other_deg 0.489 r_chiral_restr 0.071 r_gen_planes_refined 0.042 r_gen_planes_other 0.04 r_bond_refined_d 0.006 r_bond_other_d 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4923 Nucleic Acid Atoms Solvent Atoms 954 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MoRDa phasing