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Crystal Structure of the Psathyrella asperospora lectin PAL in complex with GlcNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BWR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 292 Protein at 10 mg per ml in PBS
2.4M sodium malonate pH 5.0
Crystal Properties Matthews coefficient Solvent content 3.27 62.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.55 α = 90 b = 120.55 β = 90 c = 198.95 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2014-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.979 ESRF ID29
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 2 30.91 98.5 0.078 0.996 7.8 3.1 37041 2 26.3
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 2 2.05 99.4 0.41 0.608 2.2 3
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 2bwr 2 30.91 35162 1879 97.98 0.17168 0.16936 0.1781 0.21449 0.2212 RANDOM 28.193
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] -0.77 -0.38 -0.77 2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.851 r_dihedral_angle_3_deg 13.1 r_dihedral_angle_4_deg 11.947 r_dihedral_angle_1_deg 6.147 r_long_range_B_refined 5.117 r_long_range_B_other 4.928 r_scangle_other 3.628 r_mcangle_other 2.559 r_mcangle_it 2.558 r_scbond_it 2.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.851 r_dihedral_angle_3_deg 13.1 r_dihedral_angle_4_deg 11.947 r_dihedral_angle_1_deg 6.147 r_long_range_B_refined 5.117 r_long_range_B_other 4.928 r_scangle_other 3.628 r_mcangle_other 2.559 r_mcangle_it 2.558 r_scbond_it 2.484 r_scbond_other 2.483 r_mcbond_it 1.843 r_mcbond_other 1.843 r_angle_refined_deg 1.721 r_angle_other_deg 0.998 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 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 3016 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing