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Crystal structure of a Crenomytilus grayanus lectin in complex with Gb3 allyl
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.2 M imidazole malate, 25%(w/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 2.66 53.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.043 α = 90 b = 72.464 β = 90 c = 94.361 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 CCD ADSC QUANTUM 315r 2014-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.64 30 99.1 0.111 44.1 19.9 44506
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 1.64 1.7 90.6 0.44 4.2 10.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.64 30 41184 2090 96.22 0.11978 0.11741 0.16678 0.1679 RANDOM 14.109
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] -0.18 0.18
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.774 r_dihedral_angle_2_deg 31.634 r_dihedral_angle_4_deg 20.316 r_dihedral_angle_3_deg 12.431 r_sphericity_bonded 9.103 r_dihedral_angle_1_deg 7.255 r_long_range_B_refined 4.465 r_long_range_B_other 3.735 r_scangle_other 3.16 r_rigid_bond_restr 2.857
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.774 r_dihedral_angle_2_deg 31.634 r_dihedral_angle_4_deg 20.316 r_dihedral_angle_3_deg 12.431 r_sphericity_bonded 9.103 r_dihedral_angle_1_deg 7.255 r_long_range_B_refined 4.465 r_long_range_B_other 3.735 r_scangle_other 3.16 r_rigid_bond_restr 2.857 r_scbond_it 2.67 r_scbond_other 2.67 r_angle_refined_deg 1.783 r_angle_other_deg 1.765 r_mcangle_other 1.668 r_mcangle_it 1.65 r_mcbond_it 1.429 r_mcbond_other 1.415 r_chiral_restr 0.106 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.005 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2398 Nucleic Acid Atoms Solvent Atoms 423 Heterogen Atoms 166
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SHELXCD phasing