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1.9 Angstrom Resolution Crystal Structure of dTDP-4-dehydrorhamnose Reductase from Yersinia enterocolitica
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 Protein: 7.2 mg/ml, 0.25M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: Classics II (C5), 0.96M Sodium citrate (pH 7.0); Cryo: Screen : 50% Sucrose (1:1)
Crystal Properties Matthews coefficient Solvent content 2.9 57.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.445 α = 90 b = 184.871 β = 90 c = 187.017 γ = 90
Symmetry Space Group I 2 2 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 CCD MARMOSAIC 225 mm CCD C(111) 2014-08-14 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) 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 1.9 30 99.6 0.07 0.07 28.8 7.5 179762 -3 28.2
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 1.9 1.93 96.3 0.649 0.887 2.7 6.8
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.9 29.94 169660 8981 99.57 0.16146 0.15993 0.1664 0.19066 0.1965 RANDOM 40.524
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] -2.11 4.39 -2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.252 r_dihedral_angle_4_deg 14.654 r_dihedral_angle_3_deg 8.865 r_long_range_B_refined 6.606 r_long_range_B_other 6.337 r_scangle_other 3.3 r_dihedral_angle_1_deg 2.94 r_mcangle_other 2.234 r_mcangle_it 2.233 r_scbond_it 2.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.252 r_dihedral_angle_4_deg 14.654 r_dihedral_angle_3_deg 8.865 r_long_range_B_refined 6.606 r_long_range_B_other 6.337 r_scangle_other 3.3 r_dihedral_angle_1_deg 2.94 r_mcangle_other 2.234 r_mcangle_it 2.233 r_scbond_it 2.112 r_scbond_other 2.103 r_angle_refined_deg 1.474 r_mcbond_it 1.403 r_mcbond_other 1.399 r_angle_other_deg 0.875 r_chiral_restr 0.102 r_gen_planes_refined 0.023 r_gen_planes_other 0.019 r_bond_refined_d 0.009 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13282 Nucleic Acid Atoms Solvent Atoms 1446 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing