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Crystal structure of BP39L lectin from Burkholderia pseudomallei at 1.7 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 290 0.1 M MES, 15% PEG 5000 MME, 0.2 M ammonium sulphate, pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.93 36.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.076 α = 90 b = 87.549 β = 90 c = 159.1 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2013-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.979 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.7 79.55 94.7 0.071 1 25.1 14 33933
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 95.9 0.43 0.924 6.2 14.3
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 SAD THROUGHOUT 1.7 79.55 32232 1701 94.45 0.1593 0.15737 0.1618 0.19609 0.1957 RANDOM 16.887
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] 0.33 4.57 -4.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.394 r_dihedral_angle_4_deg 16.741 r_dihedral_angle_3_deg 12.667 r_dihedral_angle_1_deg 7.79 r_long_range_B_refined 5.784 r_long_range_B_other 5.655 r_scangle_other 4.063 r_scbond_it 2.694 r_scbond_other 2.682 r_mcangle_it 2.523
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.394 r_dihedral_angle_4_deg 16.741 r_dihedral_angle_3_deg 12.667 r_dihedral_angle_1_deg 7.79 r_long_range_B_refined 5.784 r_long_range_B_other 5.655 r_scangle_other 4.063 r_scbond_it 2.694 r_scbond_other 2.682 r_mcangle_it 2.523 r_mcangle_other 2.522 r_angle_refined_deg 2.099 r_mcbond_it 1.812 r_mcbond_other 1.81 r_angle_other_deg 1.108 r_chiral_restr 0.139 r_bond_refined_d 0.023 r_gen_planes_refined 0.013 r_bond_other_d 0.007 r_gen_planes_other 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2596 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing