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Apo histidine-tagged saccharopine dehydrogenase (L-Glu forming) from Saccharomyces cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E5L PDB ENTRY 1E5L, used monomer, backbone only
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 298 1.2M Ammonium sulfate, 25mM Bis-Tris, 6.5-7mg/mL enzyme, 50mM Tris-HCl pH 8.0, 150mM KCl, 75mM imidazole, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.9 57.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.279 α = 90 b = 85.279 β = 90 c = 141.977 γ = 120
Symmetry Space Group P 31 2 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 MICRO-OPTICS 2003-08-18 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 1.7 39.85 97.6 0.056 15.8 7.18 66370 64775 2 23.6
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) 1.7 1.76 95.9 95.9 0.368 4.3 4.98 6559
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1E5L, used monomer, backbone only 1.7 39.85 2 64787 64774 3290 97.6 0.2 0.2 0.198 0.24 0.2247 RANDOM 27.461
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] 0.01 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.542 r_dihedral_angle_4_deg 15.705 r_dihedral_angle_3_deg 13.158 r_dihedral_angle_1_deg 6.018 r_scangle_it 3.483 r_mcangle_it 3.409 r_scbond_it 2.709 r_mcbond_it 2.506 r_angle_refined_deg 1.407 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.542 r_dihedral_angle_4_deg 15.705 r_dihedral_angle_3_deg 13.158 r_dihedral_angle_1_deg 6.018 r_scangle_it 3.483 r_mcangle_it 3.409 r_scbond_it 2.709 r_mcbond_it 2.506 r_angle_refined_deg 1.407 r_nbtor_refined 0.311 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.129 r_symmetry_hbond_refined 0.099 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3444 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 20
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction CCP4 data scaling ARP/wARP model building XTALVIEW refinement