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Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cervisiae complexed with NAD.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UGK PDB ID 3UGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.1M Bis-Tris Propane, 0.22M Malonate, 24% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.49 50.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.01 α = 90 b = 104.45 β = 116.6 c = 69.08 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 IMAGE PLATE RIGAKU RAXIS IV++ 2011-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
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 2.3 32.64 98.1 0.122 5.3 2.2 78060 35383 1 1.5 33.1
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 2.3 2.42 96.9 0.632 1.5 2.1 5072
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ID 3UGK 2.3 32.64 2 33594 33594 1757 97.81 0.21022 0.20711 0.2047 0.26995 0.261 RANDOM 23.513
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] -0.7 0.36 -0.49 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.648 r_dihedral_angle_4_deg 22.386 r_dihedral_angle_3_deg 17.97 r_dihedral_angle_1_deg 6.217 r_scangle_it 4.438 r_scbond_it 2.746 r_angle_refined_deg 1.885 r_mcangle_it 1.766 r_mcbond_it 0.945 r_chiral_restr 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.648 r_dihedral_angle_4_deg 22.386 r_dihedral_angle_3_deg 17.97 r_dihedral_angle_1_deg 6.217 r_scangle_it 4.438 r_scbond_it 2.746 r_angle_refined_deg 1.885 r_mcangle_it 1.766 r_mcbond_it 0.945 r_chiral_restr 0.117 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5728 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 89
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling