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Crystal structure of Medicago truncatula Histidinol-Phosphate Phosphatase (MtHPP) in complex with L-histidinol phosphate and Mg2+
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 292 Protein at 19 mg/ml concentration.
15% PEG 3350, 0.2 M diammonium hydrogen phosphate, pH 8.0. Crystal washed in a crystallization solution supplemented with 2 mM MgCl2, 5 mM HOLP and 20% glycerol and immediately vitrified in liquid nitrogen
Crystal Properties Matthews coefficient Solvent content 2.1 41.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.885 α = 90 b = 89.802 β = 97.07 c = 92.593 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 ADSC QUANTUM 315r 2015-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9793 APS 19-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 1.36 40 99.8 0.072 15 5.1 214644
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 1.36 1.44 98.8 0.82 1.9 5
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 1.36 36.25 213570 1074 99.8 0.116 0.116 0.1164 0.156 0.1567 RANDOM 17.576
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] -0.18 0.81 0.04 -0.06
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.499 r_dihedral_angle_2_deg 36.729 r_sphericity_bonded 14.752 r_dihedral_angle_4_deg 14.161 r_dihedral_angle_3_deg 13.056 r_dihedral_angle_1_deg 6.293 r_long_range_B_refined 5.784 r_long_range_B_other 5.784 r_scangle_other 4.769 r_scbond_it 3.949
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.499 r_dihedral_angle_2_deg 36.729 r_sphericity_bonded 14.752 r_dihedral_angle_4_deg 14.161 r_dihedral_angle_3_deg 13.056 r_dihedral_angle_1_deg 6.293 r_long_range_B_refined 5.784 r_long_range_B_other 5.784 r_scangle_other 4.769 r_scbond_it 3.949 r_scbond_other 3.948 r_rigid_bond_restr 3.702 r_mcangle_it 2.909 r_mcangle_other 2.909 r_mcbond_it 2.296 r_mcbond_other 2.296 r_angle_refined_deg 1.9 r_angle_other_deg 1.112 r_chiral_restr 0.137 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7967 Nucleic Acid Atoms Solvent Atoms 1315 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing