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Human spermidine synthase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 300 20% PEG 3350, 0.2M Mg(OAc)2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.13 42.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.323 α = 90 b = 60.593 β = 108.96 c = 86.667 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 100 IMAGE PLATE RIGAKU 2006-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54178
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 1.99 81.92 99.4 0.121 7.5 5.3 36969 36969
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 1.99 81.92 36969 36969 1945 98.63 0.20923 0.20923 0.2062 0.2041 0.26755 0.263 RANDOM 21.46
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] 1.25 -0.33 -0.38 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.311 r_dihedral_angle_4_deg 19.166 r_dihedral_angle_3_deg 14.717 r_dihedral_angle_1_deg 6.787 r_scangle_it 2.922 r_scbond_it 2.041 r_angle_refined_deg 1.521 r_mcangle_it 1.079 r_mcbond_it 0.718 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.311 r_dihedral_angle_4_deg 19.166 r_dihedral_angle_3_deg 14.717 r_dihedral_angle_1_deg 6.787 r_scangle_it 2.922 r_scbond_it 2.041 r_angle_refined_deg 1.521 r_mcangle_it 1.079 r_mcbond_it 0.718 r_nbtor_refined 0.3 r_symmetry_hbond_refined 0.211 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.182 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.103 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 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 4443 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing