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Structural characterization and binding studies of a plant pathogenesis related protein heamanthin from haemanthus multiflorus reveal its dual inhibitory effects against xylanase and alpha-amylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HVM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 298 0.1M ammonium sulphate, 20mM phosphate buffer, 0.1M sodium acetate, 20% PEG 6000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.27 45.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.803 α = 90 b = 65.4 β = 102 c = 49.435 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 291 IMAGE PLATE MAR scanner 345 mm plate mirror 2007-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54312
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 48.22 97.5 17702 16787
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 99
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2HVM 2 48.22 17702 16787 889 97.5 0.18 0.15372 0.15193 0.1731 0.18632 0.2149 RANDOM 26.53
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] -0.23 -0.15 -0.04 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.247 r_dihedral_angle_1_deg 4.912 r_scangle_it 4.722 r_scbond_it 2.992 r_mcangle_it 2.05 r_angle_refined_deg 1.811 r_mcbond_it 1.112 r_symmetry_hbond_refined 0.244 r_nbd_refined 0.226 r_symmetry_vdw_refined 0.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.247 r_dihedral_angle_1_deg 4.912 r_scangle_it 4.722 r_scbond_it 2.992 r_mcangle_it 2.05 r_angle_refined_deg 1.811 r_mcbond_it 1.112 r_symmetry_hbond_refined 0.244 r_nbd_refined 0.226 r_symmetry_vdw_refined 0.199 r_xyhbond_nbd_refined 0.178 r_chiral_restr 0.147 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2108 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 9
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling