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Crystal Structure of Medicago truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-aminohexanamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VKP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 70% of 37th condition of Morpheus Screen (04 mM Alcohols, 70 mM Buffer System 1 at pH 6.5, 35% Precipitant Mix 1)
Crystal Properties Matthews coefficient Solvent content 3.07 59.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.445 α = 90 b = 142.445 β = 90 c = 345.429 γ = 120
Symmetry Space Group P 61 2 2
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 RAYONIX MX300-HS 2017-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
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 2.2 50.19 94.7 0.12 0.13 0.04 0.998 13.1 7.9 80033 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.38 68.2 0.726 0.29 0.814 2.7 6.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1vkp 2.2 50.19 78801 1232 76.17 0.16603 0.16543 0.20416 0.1779 RANDOM 33.838
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] -0.32 -0.16 -0.32 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.969 r_dihedral_angle_4_deg 20.201 r_dihedral_angle_3_deg 15.796 r_dihedral_angle_1_deg 7.23 r_long_range_B_refined 6.355 r_long_range_B_other 6.332 r_scangle_other 3.974 r_mcangle_it 3.611 r_mcangle_other 3.611 r_scbond_it 2.462
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.969 r_dihedral_angle_4_deg 20.201 r_dihedral_angle_3_deg 15.796 r_dihedral_angle_1_deg 7.23 r_long_range_B_refined 6.355 r_long_range_B_other 6.332 r_scangle_other 3.974 r_mcangle_it 3.611 r_mcangle_other 3.611 r_scbond_it 2.462 r_scbond_other 2.46 r_mcbond_it 2.186 r_mcbond_other 2.185 r_angle_refined_deg 1.865 r_angle_other_deg 1.077 r_chiral_restr 0.09 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 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 11351 Nucleic Acid Atoms Solvent Atoms 773 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling PHASER phasing