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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 = 58.125 α = 90 b = 60.663 β = 108.68 c = 86.705 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 2006-03-10 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) R Sym 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 1.89 82.2 97.9 0.088 0.119 4.4 44511 44511
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1.89 82.2 42238 2255 97.15 0.17906 0.17647 0.1754 0.22751 0.225 RANDOM 22.497
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] 0.99 -0.42 -0.2 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.417 r_dihedral_angle_4_deg 17.5 r_dihedral_angle_3_deg 13.386 r_dihedral_angle_1_deg 6.671 r_scangle_it 3.54 r_scbond_it 2.403 r_angle_refined_deg 1.562 r_mcangle_it 1.394 r_mcbond_it 0.894 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.417 r_dihedral_angle_4_deg 17.5 r_dihedral_angle_3_deg 13.386 r_dihedral_angle_1_deg 6.671 r_scangle_it 3.54 r_scbond_it 2.403 r_angle_refined_deg 1.562 r_mcangle_it 1.394 r_mcbond_it 0.894 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.206 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.189 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.105 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 4427 Nucleic Acid Atoms Solvent Atoms 624 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing