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The structure of ornithine decarboxylase from Leishmania infantum in complex with PLP and DFMO
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20,000
Crystal Properties Matthews coefficient Solvent content 2.07 40.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.87 α = 90 b = 117.87 β = 90 c = 82.175 γ = 120
Symmetry Space Group P 31 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 PIXEL DECTRIS PILATUS 6M-F 2021-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.999900 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 3.3 47.89 99.9 0.204 0.22 0.081 0.998 12 13.4 10203
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.57 100 1.851 1.998 0.744 0.675 13.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.301 38.612 10186 503 99.736 0.196 0.1934 0.1988 0.2396 0.2453 124.924
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] -3.942 -1.971 -3.942 12.787
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 32.208 r_lrange_other 32.208 r_scangle_it 29.036 r_scangle_other 29.031 r_mcangle_it 26.148 r_mcangle_other 26.144 r_scbond_it 21.457 r_scbond_other 21.451 r_mcbond_it 19.703 r_mcbond_other 19.702
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 32.208 r_lrange_other 32.208 r_scangle_it 29.036 r_scangle_other 29.031 r_mcangle_it 26.148 r_mcangle_other 26.144 r_scbond_it 21.457 r_scbond_other 21.451 r_mcbond_it 19.703 r_mcbond_other 19.702 r_dihedral_angle_3_deg 16.955 r_dihedral_angle_6_deg 16.398 r_dihedral_angle_2_deg 7.969 r_dihedral_angle_1_deg 7.354 r_angle_refined_deg 2.672 r_angle_other_deg 0.816 r_symmetry_xyhbond_nbd_refined 0.295 r_nbd_refined 0.228 r_symmetry_nbd_other 0.227 r_symmetry_nbd_refined 0.222 r_nbd_other 0.215 r_nbtor_refined 0.192 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.104 r_symmetry_nbtor_other 0.095 r_ext_dist_refined_b 0.035 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3455 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction Aimless data scaling MOLREP phasing