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2-keto-3-deoxy-D-arabinonate dehydratase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 293 Na/K phosphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.815 α = 90 b = 127.815 β = 90 c = 222.366 γ = 90
Symmetry Space Group I 41 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 MARRESEARCH Rh-coated silicon mirror, silicon 111 monochromator, Rh-coated glass mirror 2005-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.97950 BESSY 14.2
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 2.1 111.11 99.4 0.094 23.1 10.4 53699 53699
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 98.7 0.582 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2.1 111.11 50918 50918 2732 99.31 0.20216 0.20128 0.2024 0.21882 0.2188 RANDOM 34.851
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] 0.72 0.72 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.677 r_dihedral_angle_4_deg 14.068 r_dihedral_angle_3_deg 12.482 r_dihedral_angle_1_deg 5.876 r_scangle_it 3.997 r_scbond_it 2.504 r_mcangle_it 1.581 r_angle_refined_deg 1.067 r_mcbond_it 0.986 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.677 r_dihedral_angle_4_deg 14.068 r_dihedral_angle_3_deg 12.482 r_dihedral_angle_1_deg 5.876 r_scangle_it 3.997 r_scbond_it 2.504 r_mcangle_it 1.581 r_angle_refined_deg 1.067 r_mcbond_it 0.986 r_nbtor_refined 0.304 r_symmetry_hbond_refined 0.218 r_nbd_refined 0.179 r_xyhbond_nbd_refined 0.161 r_symmetry_vdw_refined 0.146 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2236 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling SHELXDE phasing