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Cloning, expression, characterisation and three- dimensional structure determination of the Caenorhabditis elegans spermidine synthase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293.15 PEG 3350, Lithium sulfate, Tris-CL, Dithiothreitol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.8 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.99 α = 90 b = 99.23 β = 107.2 c = 67.85 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 75.15 CCD MARRESEARCH 2005-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.89978 SLS X06SA
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 2.5 20 94.9 0.108 25260 25260
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.65 88.77
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.5 20 24926 24926 1312 100 0.22 0.22032 0.219 0.2227 0.25415 0.2635 RANDOM 51.039
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] 8.42 2.35 -5.09 -1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.869 r_dihedral_angle_4_deg 24.032 r_dihedral_angle_3_deg 18.742 r_dihedral_angle_1_deg 7.672 r_scangle_it 7.392 r_scbond_it 5.106 r_mcangle_it 2.964 r_angle_refined_deg 1.484 r_mcbond_it 1.445 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.869 r_dihedral_angle_4_deg 24.032 r_dihedral_angle_3_deg 18.742 r_dihedral_angle_1_deg 7.672 r_scangle_it 7.392 r_scbond_it 5.106 r_mcangle_it 2.964 r_angle_refined_deg 1.484 r_mcbond_it 1.445 r_nbtor_refined 0.312 r_nbd_refined 0.219 r_symmetry_hbond_refined 0.181 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.109 r_symmetry_vdw_refined 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 4378 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data scaling