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Identificationand Characterization of an Oxalylfrom Grass pea (Lathyrus sativusCoA-Synthetase L.)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IE2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.2M NaCl
25% Polyethylene glycol (PEG) 3,350
100 mM Tris pH 8.5. T
Crystal Properties Matthews coefficient Solvent content 2.15 42.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62 α = 90 b = 74.26 β = 90 c = 101.68 γ = 90
Symmetry Space Group P 2 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 IMAGE PLATE RIGAKU RAXIS IV++ 2018-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.7 47.64 99.97 0.1858 0.851 21.7 19.7 13429 22.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.797 100 0.2636 6.76 20.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 5IE2 2.7 47.64 12807 622 99.97 0.20856 0.20755 0.2116 0.2287 0.234 RANDOM 20.496
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] 0.93 -1.4 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.478 r_dihedral_angle_4_deg 15.995 r_dihedral_angle_3_deg 13.028 r_dihedral_angle_1_deg 5.863 r_long_range_B_refined 2.032 r_long_range_B_other 2.022 r_angle_refined_deg 1.197 r_angle_other_deg 1.074 r_mcangle_it 0.899 r_mcangle_other 0.899
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.478 r_dihedral_angle_4_deg 15.995 r_dihedral_angle_3_deg 13.028 r_dihedral_angle_1_deg 5.863 r_long_range_B_refined 2.032 r_long_range_B_other 2.022 r_angle_refined_deg 1.197 r_angle_other_deg 1.074 r_mcangle_it 0.899 r_mcangle_other 0.899 r_scangle_other 0.55 r_mcbond_it 0.489 r_mcbond_other 0.486 r_scbond_it 0.28 r_scbond_other 0.279 r_chiral_restr 0.036 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3774 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing