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Crystal structure of human spermine synthase in complex with spermidine and 5-methylthioadenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O06 PDB entry 2O06
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 300 12% PEG 20000, 0.1 M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.54 51.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.385 α = 94.23 b = 74.032 β = 92.88 c = 143.226 γ = 107.07
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 var 2006-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ DW 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 50 94.3 115647 115647
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2O06 1.95 40.56 109886 109886 5758 93.96 0.2007 0.2007 0.19776 0.25744 0.2526 RANDOM 22.798
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] -0.85 -0.55 -0.13 -1.33 -0.14 1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.925 r_dihedral_angle_4_deg 17.33 r_dihedral_angle_3_deg 15.512 r_dihedral_angle_1_deg 6.964 r_scangle_it 3.819 r_scbond_it 2.587 r_mcangle_it 1.699 r_angle_refined_deg 1.667 r_mcbond_it 1.09 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.925 r_dihedral_angle_4_deg 17.33 r_dihedral_angle_3_deg 15.512 r_dihedral_angle_1_deg 6.964 r_scangle_it 3.819 r_scbond_it 2.587 r_mcangle_it 1.699 r_angle_refined_deg 1.667 r_mcbond_it 1.09 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.265 r_symmetry_vdw_refined 0.247 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.183 r_chiral_restr 0.117 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 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 10956 Nucleic Acid Atoms Solvent Atoms 1164 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing