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Crystal Structure of Oxalylglycine-bound Saccharopine Dehydrogenase (L-Lys Forming) from Saccharomyces cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q99 PDB ENTRY 2Q99 (BACKBONE ONLY)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 PEG-MME 2000, Tris, AMP, Oxalylglycine, DTT, pH 8.0, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.93 36.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.762 α = 90 b = 74.301 β = 90 c = 74.619 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 IMAGE PLATE RIGAKU RAXIS IV MICRO-OPTICS 2007-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 1.6 29.7 96.5 0.056 15.8 6.36 48196 46497 2 2 32.5
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) 1.6 1.66 87.6 0.358 3.5 5.49 4171
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2Q99 (BACKBONE ONLY) 1.6 30 48196 46484 2351 96.45 0.209 0.209 0.208 0.2005 0.241 0.2317 RANDOM 19.772
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] -0.36 1.04 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.271 r_dihedral_angle_4_deg 13.177 r_dihedral_angle_3_deg 11.809 r_dihedral_angle_1_deg 5.319 r_scangle_it 2.968 r_scbond_it 2.01 r_angle_refined_deg 1.328 r_mcangle_it 1.254 r_mcbond_it 0.779 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.271 r_dihedral_angle_4_deg 13.177 r_dihedral_angle_3_deg 11.809 r_dihedral_angle_1_deg 5.319 r_scangle_it 2.968 r_scbond_it 2.01 r_angle_refined_deg 1.328 r_mcangle_it 1.254 r_mcbond_it 0.779 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.246 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.183 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2916 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 10
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction ARP/wARP model building