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Crystal Structure of Medicago truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KAE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 292 100 mM MES pH 5.2, 200 mM NACl, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.859 α = 90 b = 139.201 β = 119.18 c = 102.692 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX300-HS 2016-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97625 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.97 48.73 99.4 0.078 13.7 6.14 175983
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.09 97.4 0.905 1.9 5.7
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 FREE R-VALUE 1kae 1.97 48.73 174751 1232 99.57 0.17888 0.17853 0.1854 0.22912 0.2279 RANDOM 47.206
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] 0.05 0.22 -0.38 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.009 r_dihedral_angle_3_deg 15.111 r_dihedral_angle_4_deg 14.857 r_dihedral_angle_1_deg 6.321 r_long_range_B_refined 5.519 r_long_range_B_other 5.494 r_scangle_other 3.536 r_mcangle_it 2.811 r_mcangle_other 2.811 r_scbond_it 2.167
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.009 r_dihedral_angle_3_deg 15.111 r_dihedral_angle_4_deg 14.857 r_dihedral_angle_1_deg 6.321 r_long_range_B_refined 5.519 r_long_range_B_other 5.494 r_scangle_other 3.536 r_mcangle_it 2.811 r_mcangle_other 2.811 r_scbond_it 2.167 r_scbond_other 2.167 r_mcbond_it 1.791 r_mcbond_other 1.791 r_angle_refined_deg 1.693 r_angle_other_deg 1.014 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 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 19688 Nucleic Acid Atoms Solvent Atoms 625 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling BALBES phasing