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Crystal structure of Parkia biglobosa seed lectin (PBL) in complex with methyl alpha D-mannopyranoside
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 310 NaCl 0.1 M, Bicine 0.1 M, PEG 550 25%, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Crystal Properties Matthews coefficient Solvent content 2.26 45.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.139 α = 90 b = 86.659 β = 90 c = 127.857 γ = 90
Symmetry Space Group C 2 2 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 CCD MARMOSAIC 225 mm CCD 2013-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.4590 LNLS W01B-MX2
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 2.12 43.33 94.71 22080
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2.12 43.33 22080 22080 1197 94.73 0.25992 0.25813 0.2581 0.29272 0.2919 RANDOM 46.245
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] -0.03 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.196 r_dihedral_angle_3_deg 19.297 r_dihedral_angle_4_deg 12.588 r_dihedral_angle_1_deg 7.399 r_scangle_it 3.679 r_scbond_it 2.46 r_mcangle_it 2.375 r_angle_refined_deg 1.905 r_mcbond_it 1.609 r_chiral_restr 0.373
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.196 r_dihedral_angle_3_deg 19.297 r_dihedral_angle_4_deg 12.588 r_dihedral_angle_1_deg 7.399 r_scangle_it 3.679 r_scbond_it 2.46 r_mcangle_it 2.375 r_angle_refined_deg 1.905 r_mcbond_it 1.609 r_chiral_restr 0.373 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3310 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 39
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling