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Crystal structure of Medicago truncatula Histidinol-Phosphate Phosphatase (MtHPP) with intermolecular cross-link between Lys158 and Cys245
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 30% PEG 3350, 0.1 M Bis-Tris pH 6.5, 0.2 M ammonium acetate, 10 mM magnesium acetate.
Crystals were incubated overnight over the reservoir supplemented with 100 mM formaldehyde to complete cross-linking between Lys158 and Cys245 and vitrified in Paraton-N
Crystal Properties Matthews coefficient Solvent content 2.09 41.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.24 α = 90 b = 89.39 β = 96.93 c = 92.24 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 2015-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.7999 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 1.32 40 99.9 0.065 12 5.1 234185
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 1.32 1.35 99.9 0.71 2 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.32 36.2 231842 2342 99.87 0.125 0.124 0.1238 0.165 0.1635 RANDOM 23.274
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] 0.74 -0.29 -0.02 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.946 r_sphericity_free 36.321 r_sphericity_bonded 15.491 r_dihedral_angle_4_deg 14.744 r_dihedral_angle_3_deg 13.36 r_dihedral_angle_1_deg 6.178 r_long_range_B_refined 5.687 r_long_range_B_other 4.943 r_scangle_other 4.505 r_rigid_bond_restr 4.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.946 r_sphericity_free 36.321 r_sphericity_bonded 15.491 r_dihedral_angle_4_deg 14.744 r_dihedral_angle_3_deg 13.36 r_dihedral_angle_1_deg 6.178 r_long_range_B_refined 5.687 r_long_range_B_other 4.943 r_scangle_other 4.505 r_rigid_bond_restr 4.223 r_scbond_it 3.807 r_scbond_other 3.807 r_mcangle_other 3.059 r_mcangle_it 3.058 r_mcbond_it 2.564 r_mcbond_other 2.559 r_angle_refined_deg 2 r_angle_other_deg 1.213 r_chiral_restr 0.15 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7891 Nucleic Acid Atoms Solvent Atoms 1071 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing