☰ Navigation Tabs
Crystal Structure of D-isomer specific 2-hydroxyacid dehydrogenase from Lactobacillus delbrueckii ssp. bulgaricus: NAD complexed form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DXY PDB ENTRY 1DXY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 25% PEG 3350, 200MM MGCL2, 100MM HEPES PH7.5
Crystal Properties Matthews coefficient Solvent content 3.14 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.718 α = 90 b = 110.012 β = 90 c = 147.736 γ = 90
Symmetry Space Group P 21 21 21
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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.75 49.24 99.5 0.1 12.7 4.7 39722
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 2.75 2.9 99.9 0.56 2.6 4.8
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 PDB ENTRY 1DXY 2.75 44.99 37669 1953 99.1 0.19122 0.18763 0.1884 0.25895 0.2597 RANDOM 47.897
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] -2.7 3.65 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.898 r_dihedral_angle_4_deg 23.654 r_dihedral_angle_3_deg 19.826 r_dihedral_angle_1_deg 6.999 r_angle_refined_deg 1.678 r_chiral_restr 0.113 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.898 r_dihedral_angle_4_deg 23.654 r_dihedral_angle_3_deg 19.826 r_dihedral_angle_1_deg 6.999 r_angle_refined_deg 1.678 r_chiral_restr 0.113 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10154 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing