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CRYSTAL STRUCTURE OF RECOMBINANT DIOCLEA GRANDIFLORA LECTIN COMPLEXED WITH 5-BROMO-4-CHLORO-3-INDOLYL-A-D-MANNOSE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DGL PDB ENTRY 1DGL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 CRYSTALS WERE GROWN BY THE HANGING DROP VAPOUR DIFFUSION METHOD USING 15% PEG 4000, 0.1M HEPES, PH 7.5 AND 0.1M LITHIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 2.62 53.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.171 α = 90 b = 85.153 β = 90 c = 175.741 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 MARRESEARCH 2006-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 2.1 72.17 99.9 0.08 6.9 4.6 63973 2
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 2.1 2.21 99.7 0.3 2.1 4
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DGL 2.1 87.71 60684 3234 99.8 0.19 0.187 0.189 0.239 RANDOM 24.47
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] 0.01 0.86 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.534 r_dihedral_angle_3_deg 14.486 r_dihedral_angle_4_deg 14.171 r_dihedral_angle_1_deg 7.709 r_angle_refined_deg 1.573 r_nbtor_refined 0.299 r_symmetry_hbond_refined 0.281 r_symmetry_vdw_refined 0.208 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.534 r_dihedral_angle_3_deg 14.486 r_dihedral_angle_4_deg 14.171 r_dihedral_angle_1_deg 7.709 r_angle_refined_deg 1.573 r_nbtor_refined 0.299 r_symmetry_hbond_refined 0.281 r_symmetry_vdw_refined 0.208 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.109 r_metal_ion_refined 0.083 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 7235 Nucleic Acid Atoms Solvent Atoms 441 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling MOLREP phasing