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Crystal structure of lysine/ornithine decarboxylase complexed with cadaverine from Vibrio vulnificus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F3T PDB ENTRY 1F3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.4 277 30% PEG-4000, 0.1M Tris HCl pH8.4, 0.2M Magnesium chloride, 0.5% w/v n-octyl-b-D-glucoside , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.1 41.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.245 α = 90 b = 88.027 β = 90 c = 99.272 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 SBC-3 2006-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.979269 APS 19-BM
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 2.14 50 90.6 0.107 0.107 14.6 4.4 37184 1.4 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.19 87.7 0.429 0.429 2 2.7
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 (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 1F3T 2.14 24.81 35254 35254 1882 89.91 0.17791 0.17451 0.1935 0.24003 0.2514 RANDOM 26.185
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] 2.51 0.08 -2.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.089 r_dihedral_angle_4_deg 17.6 r_dihedral_angle_3_deg 16.005 r_dihedral_angle_1_deg 6.451 r_scangle_it 2.99 r_scbond_it 1.886 r_angle_refined_deg 1.517 r_mcangle_it 1.171 r_mcbond_it 0.699 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.089 r_dihedral_angle_4_deg 17.6 r_dihedral_angle_3_deg 16.005 r_dihedral_angle_1_deg 6.451 r_scangle_it 2.99 r_scbond_it 1.886 r_angle_refined_deg 1.517 r_mcangle_it 1.171 r_mcbond_it 0.699 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.285 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.186 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.095 r_bond_refined_d 0.014 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 5666 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing