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Crystal structure of snake gourd seed lectin in complex with lactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HR6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 300 reservoir solution contained 4M sodium formate
Crystal Properties Matthews coefficient Solvent content 3.51 64.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.429 α = 90 b = 109.429 β = 90 c = 232.668 γ = 120
Symmetry Space Group P 61 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 CCD MARMOSAIC 225 mm CCD 2015-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9537 ESRF BM14
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 3.05 94.77 100 0.146 0.99 13.3 18.9 16493
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 3.05 3.21 100 1.534 0.808 2 19.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 4HR6 3.05 94.77 15645 782 99.97 0.22287 0.22154 0.2378 0.25067 0.2556 RANDOM 118.829
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] 1.69 0.84 1.69 -5.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.795 r_dihedral_angle_3_deg 15.964 r_dihedral_angle_4_deg 13.956 r_long_range_B_other 13.721 r_long_range_B_refined 13.72 r_scangle_other 9.169 r_dihedral_angle_1_deg 7.225 r_mcangle_it 7.072 r_mcangle_other 7.071 r_scbond_it 6.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.795 r_dihedral_angle_3_deg 15.964 r_dihedral_angle_4_deg 13.956 r_long_range_B_other 13.721 r_long_range_B_refined 13.72 r_scangle_other 9.169 r_dihedral_angle_1_deg 7.225 r_mcangle_it 7.072 r_mcangle_other 7.071 r_scbond_it 6.138 r_scbond_other 6.137 r_mcbond_it 4.69 r_mcbond_other 4.69 r_angle_refined_deg 1.959 r_angle_other_deg 1.169 r_chiral_restr 0.113 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.003 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 3974 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing