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Crystal structure of Dioclea rostrata lectin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H9W PDB ENTRY 1H9W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M Na-HEPES pH 7.5-8.5, 0.4-1.2M sodium potassium tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.33 47.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.511 α = 90 b = 88.22 β = 90 c = 87.764 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 CCD MAR CCD 165 mm M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 LNLS D03B-MX1
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 2.05 33.15 93 0.067 2.1 9.4 15297 14526 2 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) 2.05 2.103 99.8 0.341 2.1
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 PDB ENTRY 1H9W 2.05 33.11 14526 766 99.65 0.18936 0.18679 0.1903 0.2379 0.2402 RANDOM 25.309
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.64 r_dihedral_angle_4_deg 19.227 r_dihedral_angle_3_deg 17.189 r_dihedral_angle_1_deg 7.974 r_angle_refined_deg 1.986 r_symmetry_hbond_refined 0.481 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.267 r_nbd_refined 0.238 r_xyhbond_nbd_refined 0.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.64 r_dihedral_angle_4_deg 19.227 r_dihedral_angle_3_deg 17.189 r_dihedral_angle_1_deg 7.974 r_angle_refined_deg 1.986 r_symmetry_hbond_refined 0.481 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.267 r_nbd_refined 0.238 r_xyhbond_nbd_refined 0.237 r_chiral_restr 0.13 r_metal_ion_refined 0.121 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 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_scbond_it 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 1764 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 7
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction