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Crystal structure of CV39L lectin from Chromobacterium violaceum at 1.8 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 290 0.1 M sodium acetate, 25% PEG 4000, 0.2M ammonium sulphate, pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.18 43.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.709 α = 90 b = 123.781 β = 90 c = 180.935 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 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) 0.967 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 1.8 80.93 100 0.102 0.999 14.7 7.5 137285
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 1.8 1.9 100 0.363 0.953 4.9 7.5
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 SAD THROUGHOUT 1.8 73.04 130295 6893 99.96 0.15458 0.15279 0.1527 0.18852 0.1829 RANDOM 12.009
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] 1.64 -1.67 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.232 r_dihedral_angle_4_deg 28.84 r_dihedral_angle_3_deg 11.647 r_dihedral_angle_1_deg 7.404 r_long_range_B_refined 4.354 r_long_range_B_other 4.168 r_scangle_other 3.132 r_scbond_it 2.202 r_scbond_other 2.202 r_angle_refined_deg 2.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.232 r_dihedral_angle_4_deg 28.84 r_dihedral_angle_3_deg 11.647 r_dihedral_angle_1_deg 7.404 r_long_range_B_refined 4.354 r_long_range_B_other 4.168 r_scangle_other 3.132 r_scbond_it 2.202 r_scbond_other 2.202 r_angle_refined_deg 2.014 r_mcangle_it 1.77 r_mcangle_other 1.77 r_mcbond_it 1.236 r_mcbond_other 1.234 r_angle_other_deg 1.115 r_chiral_restr 0.145 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.006 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10790 Nucleic Acid Atoms Solvent Atoms 1275 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing