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Crystal Structure of Medicago truncatula L-Histidinol Dehydrogenase in Complex with Imidazole
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 6.5 292 Molecular Dimensions Morpheus Condition H1: 0.1 M Amino acids, 0.1 M Buffer System 1 pH 6.5, 50 % v/v Precipitant Mix 1
Crystal Properties Matthews coefficient Solvent content 2.38 48.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.752 α = 90 b = 142.814 β = 120.16 c = 105.357 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 2015-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 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 2.25 38.52 94.7 0.077 15.7 5.15 120737
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 2.25 2.39 73.8 0.611 2.06
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 1kae 2.25 38.52 119527 1208 94.94 0.18159 0.18106 0.1861 0.23388 0.2359 RANDOM 42.071
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] 0.42 -0.35 0.63 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.59 r_dihedral_angle_3_deg 16.819 r_dihedral_angle_4_deg 13.814 r_dihedral_angle_1_deg 6.384 r_long_range_B_refined 4.694 r_long_range_B_other 4.693 r_scangle_other 2.993 r_mcangle_it 2.407 r_mcangle_other 2.407 r_scbond_it 1.781
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.59 r_dihedral_angle_3_deg 16.819 r_dihedral_angle_4_deg 13.814 r_dihedral_angle_1_deg 6.384 r_long_range_B_refined 4.694 r_long_range_B_other 4.693 r_scangle_other 2.993 r_mcangle_it 2.407 r_mcangle_other 2.407 r_scbond_it 1.781 r_scbond_other 1.781 r_angle_refined_deg 1.647 r_mcbond_it 1.474 r_mcbond_other 1.474 r_angle_other_deg 1.022 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 19734 Nucleic Acid Atoms Solvent Atoms 656 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling BALBES phasing