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A structural insight into the inhibition of human and Leishmania donovani ornithine decarboxylases by 3-aminooxy-1-aminopropane
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D7K PDB entry 1D7K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 288.15 25% PEG3350, 0.2 M ammonium acetate, O.1M MES, 2mM XAP, 0.3 % cadaverine, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 288.15K
Crystal Properties Matthews coefficient Solvent content 2.92 57.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.018 α = 90 b = 87.11 β = 91.02 c = 130.08 γ = 90
Symmetry Space Group C 1 2 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 CCD MAR CCD 165 mm 2006-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 MAX II I911-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 29.45 97.8 5 92938 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.949 93.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1D7K 1.9 29.45 2 92938 85203 9468 100 0.18717 0.18422 0.1834 0.21345 0.2111 RANDOM 24.566
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] -0.13 -0.87 0.99 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.262 r_dihedral_angle_4_deg 17.852 r_dihedral_angle_3_deg 14.298 r_dihedral_angle_1_deg 5.689 r_scangle_it 2.692 r_scbond_it 1.691 r_angle_refined_deg 1.179 r_mcangle_it 1.153 r_mcbond_it 0.72 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.262 r_dihedral_angle_4_deg 17.852 r_dihedral_angle_3_deg 14.298 r_dihedral_angle_1_deg 5.689 r_scangle_it 2.692 r_scbond_it 1.691 r_angle_refined_deg 1.179 r_mcangle_it 1.153 r_mcbond_it 0.72 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.204 r_nbd_refined 0.191 r_symmetry_hbond_refined 0.174 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 6559 Nucleic Acid Atoms Solvent Atoms 523 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XSCALE data scaling PHASER phasing