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D-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with 2-ketohexanoic acid and NAD+ (1.35 A resolution)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 290 Protein buffer: 20 mM Tris-HCl pH8, 3 mM EDTA and 1 M NaCl
Crystallisation conditions: 0.1M Tris-HCl pH8, 0.5 M magnesium acetate and 20 % PEG3350
Ligands: 5 mM NAD+ and 50 mM 2-ketohexanoic acid
Crystal Properties Matthews coefficient Solvent content 2.54 51.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.455 α = 109.11 b = 75.008 β = 107.55 c = 77.555 γ = 95.91
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 ADSC QUANTUM 315 2008-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97204 Diamond I02
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 1.35 46.54 93 0.061 23.6 2.1 268611
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 1.35 1.37 91.7 0.462 2.1 2.2
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.35 46.54 219914 11807 80.19 0.12817 0.1264 0.1307 0.16174 0.1651 RANDOM 17.066
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] 0.19 -0.1 -0.1 0.18 0.07 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.952 r_sphericity_free 27.887 r_sphericity_bonded 21.444 r_dihedral_angle_4_deg 17.315 r_rigid_bond_restr 14.562 r_dihedral_angle_3_deg 10.546 r_scbond_other 6.955 r_scbond_it 6.946 r_dihedral_angle_1_deg 5.89 r_scangle_other 5.792
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.952 r_sphericity_free 27.887 r_sphericity_bonded 21.444 r_dihedral_angle_4_deg 17.315 r_rigid_bond_restr 14.562 r_dihedral_angle_3_deg 10.546 r_scbond_other 6.955 r_scbond_it 6.946 r_dihedral_angle_1_deg 5.89 r_scangle_other 5.792 r_long_range_B_refined 5.655 r_long_range_B_other 5.161 r_mcangle_other 3.065 r_mcangle_it 3.064 r_mcbond_other 2.825 r_mcbond_it 2.824 r_angle_refined_deg 1.502 r_angle_other_deg 1.423 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 9360 Nucleic Acid Atoms Solvent Atoms 1738 Heterogen Atoms 346
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing