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Crystal structure of a probable spermidine synthase from Corynebacterium glutamicum ATCC 13032
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 0.2M Potassium sodium tartrate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.13 42.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.909 α = 90 b = 65.009 β = 90 c = 87.308 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 315 Mirror 2008-11-23 M SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97915 APS 19-ID
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 1.47 23 99.4 0.068 43.5 8.2 51371 51371
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.47 1.5 95.6 0.482 2.88 6.6 2418
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 SAD THROUGHOUT 1.47 22.62 48639 48639 2614 99.28 0.1588 0.1588 0.15704 0.1545 0.19152 0.1872 RANDOM 20.23
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 0.04 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.834 r_dihedral_angle_4_deg 17.204 r_dihedral_angle_3_deg 12.74 r_sphericity_free 6.758 r_dihedral_angle_1_deg 6.159 r_scangle_it 4.535 r_sphericity_bonded 4.15 r_scbond_it 3.14 r_mcangle_it 2.231 r_rigid_bond_restr 1.702
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.834 r_dihedral_angle_4_deg 17.204 r_dihedral_angle_3_deg 12.74 r_sphericity_free 6.758 r_dihedral_angle_1_deg 6.159 r_scangle_it 4.535 r_sphericity_bonded 4.15 r_scbond_it 3.14 r_mcangle_it 2.231 r_rigid_bond_restr 1.702 r_angle_refined_deg 1.459 r_mcbond_it 1.454 r_chiral_restr 0.11 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2251 Nucleic Acid Atoms Solvent Atoms 388 Heterogen Atoms
Software Software Software Name Purpose SBC-Collect data collection SHELXD phasing MLPHARE phasing DM model building ARP/wARP model building HKL-3000 phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling DM phasing