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Structure of Helix Pomatia agglutinin with Tn antigen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CE6 PDB ENTRY 2CE6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP HANGING DROP METHOD WITH PRECIPITATION SOLUTION CONTAINING LITHIUM SULPHATE (2 M) AND AMMONIUM SULPHATE (3.5 M) IN SODIUM CITRATE BUFFER (1.5M, PH 6.5) AND 10MM TN ANTIGEN.
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.1 α = 90 b = 62.1 β = 90 c = 106.2 γ = 120
Symmetry Space Group P 63 2 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 CCD MIRROR 2000-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.8 30 93.1 0.05 19.2 7.3 3132
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 2.8 2.9 95.2 0.36 4.6
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 2CE6 2.8 20 2958 130 93.3 0.244 0.242 0.2425 0.29 0.3034 RANDOM 64.46
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] -3.6 -1.8 -3.6 5.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.239 r_angle_refined_deg 1.004 r_scangle_it 1.004 r_angle_other_deg 0.698 r_mcangle_it 0.577 r_scbond_it 0.545 r_symmetry_vdw_refined 0.387 r_mcbond_it 0.31 r_symmetry_vdw_other 0.214 r_nbd_other 0.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.239 r_angle_refined_deg 1.004 r_scangle_it 1.004 r_angle_other_deg 0.698 r_mcangle_it 0.577 r_scbond_it 0.545 r_symmetry_vdw_refined 0.387 r_mcbond_it 0.31 r_symmetry_vdw_other 0.214 r_nbd_other 0.197 r_xyhbond_nbd_refined 0.186 r_nbd_refined 0.182 r_symmetry_hbond_refined 0.099 r_nbtor_other 0.081 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 774 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing