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Crystal structure of human spermine synthase in complex with spermine and 5-methylthioadenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C6K PDB entry 3C6K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 300 18% PEG 3350, 0.1 M NaCl, 0.1 M Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.58 52.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.262 α = 90 b = 88.262 β = 90 c = 197.668 γ = 120
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 2.45 50 97.2 61292 61292
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 3C6K 2.45 35.65 58198 58198 3045 97.12 0.2117 0.2117 0.2086 0.2062 0.27092 0.2653 RANDOM 29.348
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] 1.03 0.51 1.03 -1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.353 r_dihedral_angle_4_deg 19.66 r_dihedral_angle_3_deg 17.164 r_dihedral_angle_1_deg 6.277 r_scangle_it 2.457 r_scbond_it 1.63 r_angle_refined_deg 1.478 r_mcangle_it 1.134 r_mcbond_it 0.662 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.353 r_dihedral_angle_4_deg 19.66 r_dihedral_angle_3_deg 17.164 r_dihedral_angle_1_deg 6.277 r_scangle_it 2.457 r_scbond_it 1.63 r_angle_refined_deg 1.478 r_mcangle_it 1.134 r_mcbond_it 0.662 r_nbtor_refined 0.311 r_nbd_refined 0.215 r_symmetry_hbond_refined 0.213 r_symmetry_vdw_refined 0.165 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.093 r_bond_refined_d 0.013 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 9942 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing