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Crystal structure of Concanavalin A bound to an octa-alpha-mannosyl-octasilsesquioxane cluster
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SCR PDB ENTRY 1SCR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 294.15 12% PEG 2K MME, 1mM Manganese Chloride, 1mM Calcium Chloride, 100mM HEPES pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K
Crystal Properties Matthews coefficient Solvent content 2.34 47.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.89 α = 90 b = 63.68 β = 93.23 c = 125.8 γ = 90
Symmetry Space Group P 1 21 1
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 270 TOROIDAL FOCUSING MIRROR 2010-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.95370 NSLS X6A
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 1.7 31.84 96.1 0.076 13.9 6.2 104059 100001
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 1.7 1.79 88 0.657 2.3 5.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1SCR 1.7 31.84 98996 94987 4961 95.95 0.21942 0.21942 0.21783 0.2201 0.24832 0.2478 RANDOM 20.338
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] -1.18 0.01 3.12 -1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.03 r_dihedral_angle_4_deg 16.61 r_dihedral_angle_3_deg 14.351 r_dihedral_angle_1_deg 7.703 r_scangle_it 4.417 r_scbond_it 2.942 r_mcangle_it 2.206 r_angle_refined_deg 1.986 r_mcbond_it 1.312 r_angle_other_deg 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.03 r_dihedral_angle_4_deg 16.61 r_dihedral_angle_3_deg 14.351 r_dihedral_angle_1_deg 7.703 r_scangle_it 4.417 r_scbond_it 2.942 r_mcangle_it 2.206 r_angle_refined_deg 1.986 r_mcbond_it 1.312 r_angle_other_deg 1.04 r_mcbond_other 0.38 r_chiral_restr 0.116 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7111 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 56
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling