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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 2.47 50.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.096 α = 90 b = 135.239 β = 90 c = 83.321 γ = 90
Symmetry Space Group C 2 2 21
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 2006-02-21 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 2 33.81 99.9 0.143 5.8 7.1 45882 45882
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 33.81 43549 43549 2312 99.88 0.1698 0.1698 0.1675 0.169 0.21298 0.2141 RANDOM 22.328
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.864 r_dihedral_angle_4_deg 15.539 r_dihedral_angle_3_deg 12.605 r_dihedral_angle_1_deg 6.274 r_scangle_it 2.868 r_scbond_it 1.839 r_angle_refined_deg 1.351 r_mcangle_it 1.093 r_mcbond_it 0.682 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.864 r_dihedral_angle_4_deg 15.539 r_dihedral_angle_3_deg 12.605 r_dihedral_angle_1_deg 6.274 r_scangle_it 2.868 r_scbond_it 1.839 r_angle_refined_deg 1.351 r_mcangle_it 1.093 r_mcbond_it 0.682 r_nbtor_refined 0.3 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.136 r_symmetry_hbond_refined 0.12 r_chiral_restr 0.092 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 4636 Nucleic Acid Atoms Solvent Atoms 459 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing