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native structure of conglutinin carbohydrate recognition domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RYM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 2.5 M ammonium sulfate, 0.1 M tris
Crystal Properties Matthews coefficient Solvent content 2.33 47.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.17 α = 90 b = 50.17 β = 90 c = 52.247 γ = 90
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 2007-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.92 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 0.974 50.17 81.2 0.05 0.05 0.059 22.9 7.7 61295
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.97 1.02 20.5 0.216 0.216 0.315 3.2 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 FREE R-VALUE 6RYM 0.974 50 58175 3086 81.13 0.1349 0.1347 0.1423 0.1388 0.148 RANDOM 14.148
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] -0.25 -0.25 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.741 r_dihedral_angle_4_deg 13.245 r_dihedral_angle_3_deg 11.609 r_rigid_bond_restr 7.733 r_dihedral_angle_1_deg 6.37 r_angle_refined_deg 1.654 r_angle_other_deg 1.568 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.741 r_dihedral_angle_4_deg 13.245 r_dihedral_angle_3_deg 11.609 r_rigid_bond_restr 7.733 r_dihedral_angle_1_deg 6.37 r_angle_refined_deg 1.654 r_angle_other_deg 1.568 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 896 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 1
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing