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Clitocybe nebularis ricin B-like lectin (CNL) in complex with lactose, crystallized at pH 7.1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NBC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 293 0.085M HEPES sodium, 1.7%(v/v) PEG 400, 2.0M Ammonium sulfate, 19%(w/v) Glycerol, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.82 56.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.119 α = 90 b = 85.08 β = 90 c = 97.629 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 MAR CCD 165 mm Collimating and focusing, Pt-coated mirrors 2009-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.033 ELETTRA 5.2R
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 1.14 23.03 98.3 0.06 11.5 8.5 130730 128514 1 1
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 1.14 1.16 65.6 0.326 5 4260
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3NBC 1.15 23.03 130730 128492 6458 99.51 0.142 0.139 0.138 0.16 0.1681 RANDOM 15.915
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] 0.33 -0.01 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.059 r_dihedral_angle_4_deg 19.342 r_dihedral_angle_3_deg 10.972 r_dihedral_angle_1_deg 8.566 r_scangle_it 6.829 r_scbond_it 4.863 r_mcangle_it 3.427 r_mcbond_it 2.361 r_angle_refined_deg 2.231 r_rigid_bond_restr 2.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.059 r_dihedral_angle_4_deg 19.342 r_dihedral_angle_3_deg 10.972 r_dihedral_angle_1_deg 8.566 r_scangle_it 6.829 r_scbond_it 4.863 r_mcangle_it 3.427 r_mcbond_it 2.361 r_angle_refined_deg 2.231 r_rigid_bond_restr 2.226 r_angle_other_deg 1.689 r_mcbond_other 0.946 r_chiral_restr 0.816 r_bond_refined_d 0.05 r_bond_other_d 0.038 r_gen_planes_refined 0.013 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2238 Nucleic Acid Atoms Solvent Atoms 535 Heterogen Atoms 71
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection AMoRE phasing