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D-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with 2-keto-hexanoic acid and NADP+ (1.4 A resolution)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MH6
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 condition: 0.1 M Tris-HCl pH8, 0.5 M magnesium acetate and 18 % PEG3350
Ligands: 5 mM NADP+ and 50 mM 2-keto-hexanoic acid
Crystal Properties Matthews coefficient Solvent content 2.69 54.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.53 α = 90 b = 87.4 β = 96.34 c = 66.1 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315 2009-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9507 Diamond I03
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 1.4 52.51 95.5 0.036 15.4 7.7 132820
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 1.4 1.42 91.5 0.377 2.4 8 6288
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 5MH6 1.4 52.51 125480 6675 95.24 0.13746 0.13587 0.1347 0.16701 0.1663 RANDOM 20.538
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] -0.88 0.1 -0.31 1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.918 r_sphericity_bonded 27.574 r_sphericity_free 26.866 r_dihedral_angle_4_deg 19.89 r_rigid_bond_restr 12.361 r_dihedral_angle_3_deg 12.035 r_scbond_it 9.528 r_scbond_other 9.493 r_scangle_other 8.963 r_long_range_B_refined 7.947
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.918 r_sphericity_bonded 27.574 r_sphericity_free 26.866 r_dihedral_angle_4_deg 19.89 r_rigid_bond_restr 12.361 r_dihedral_angle_3_deg 12.035 r_scbond_it 9.528 r_scbond_other 9.493 r_scangle_other 8.963 r_long_range_B_refined 7.947 r_long_range_B_other 7.946 r_mcbond_it 6.573 r_mcbond_other 6.573 r_mcangle_it 6.311 r_mcangle_other 6.31 r_dihedral_angle_1_deg 6.198 r_angle_refined_deg 1.588 r_angle_other_deg 1.315 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 4698 Nucleic Acid Atoms Solvent Atoms 676 Heterogen Atoms 145
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling Coot model building