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cDNA cloning and 1.75A crystal structure determination of PPL2, a novel chimerolectin from Parkia platycephala seeds exhibiting endochitinolytic activity
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.2 M ammonium acetate, 0,1 M trisodium citrate dehydrate, pH 5.6 and 30% (w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.15 42.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.19 α = 90 b = 59.949 β = 90 c = 76.697 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 180 mm plate 2004-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.43 LNLS D03B-MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.73 32.31 27 0.04 0.04 20.8 3.7 25805 25805
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) 1.73 1.83 0.228 8.1 3.6 12669
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1.73 32.31 2 24487 23017 1285 94.74 0.2046 0.1749 0.16888 0.1682 0.19873 0.198 RANDOM 14.678
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.035 r_dihedral_angle_4_deg 15.484 r_dihedral_angle_3_deg 13.565 r_dihedral_angle_1_deg 6.679 r_scangle_it 3.407 r_scbond_it 2.186 r_angle_refined_deg 1.485 r_mcangle_it 1.444 r_mcbond_it 0.81 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.035 r_dihedral_angle_4_deg 15.484 r_dihedral_angle_3_deg 13.565 r_dihedral_angle_1_deg 6.679 r_scangle_it 3.407 r_scbond_it 2.186 r_angle_refined_deg 1.485 r_mcangle_it 1.444 r_mcbond_it 0.81 r_nbtor_refined 0.321 r_symmetry_vdw_refined 0.288 r_symmetry_hbond_refined 0.242 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2086 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 20
Software Software Software Name Purpose MAR345 data collection SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling