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Structure of cofactor pyridoxal 5-phosphate bound human ornithine decarboxylase in complex with citrate at the catalytic center
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OO0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 100 mM tri-sodium citrate pH 5.0 and 30% polyethylene glycol monomethyl
ether 550
Crystal Properties Matthews coefficient Solvent content 2.64 53.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.54 α = 90 b = 86.47 β = 90 c = 154.56 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 PIXEL DECTRIS EIGER X 16M 2020-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.9787 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.64 43.2496 100 0.99 19.2 8.2 122761
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.68 0.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2oo0 1.66 43.2496 1.35 118401 8383 99.99 0.1798 0.1785 0.1807 0.1975 0.1988 26.8266
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.42 f_angle_d 1.315 f_chiral_restr 0.085 f_bond_d 0.013 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6284 Nucleic Acid Atoms Solvent Atoms 501 Heterogen Atoms 56
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction Aimless data scaling PHASER phasing