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Lectin Domain of Lectinolysin complexed with Glycerol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J1R PDB entry 2J1R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 294 2M MgSO4, 100mM Tris, pH 8.5, vapor diffusion, hanging drop, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.29 62.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.189 α = 90 b = 67.189 β = 90 c = 98.322 γ = 90
Symmetry Space Group P 43 21 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 ADSC QUANTUM 315 mirrors 2008-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 1.00 APS 14-BM-C
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 1.9 29.46 91.5 0.091 10.5 15.9 16856
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 1.9 1.97 72.3 0.556 13.8
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 2J1R 1.91 29.46 15702 844 90.92 0.17612 0.17457 0.1749 0.2057 0.2112 RANDOM 25.947
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] -0.57 -0.57 1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.145 r_dihedral_angle_3_deg 13.891 r_dihedral_angle_4_deg 8.84 r_dihedral_angle_1_deg 6.424 r_scangle_it 4.246 r_scbond_it 2.519 r_mcangle_it 1.677 r_angle_refined_deg 1.466 r_mcbond_it 0.909 r_chiral_restr 0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.145 r_dihedral_angle_3_deg 13.891 r_dihedral_angle_4_deg 8.84 r_dihedral_angle_1_deg 6.424 r_scangle_it 4.246 r_scbond_it 2.519 r_mcangle_it 1.677 r_angle_refined_deg 1.466 r_mcbond_it 0.909 r_chiral_restr 0.133 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_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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1107 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 8
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection