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Crystal structure of the Staphylococcal superantigen-like protein SSL5 in complex with sialyl-Lewis X at pH 7.4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M4V PDB ENTRY 1M4V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 291 20% PEG 3340, 0.2M disodium tartrate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.31 62.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.223 α = 90 b = 52.223 β = 90 c = 236.657 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 110 IMAGE PLATE MAR scanner 345 mm plate mirrors 2006-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.75 59.164 99.9 0.129 0.129 5 7.4 9300
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.9 100 0.484 0.484 1.5 7.8 1301
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 1M4V 2.75 35.07 8789 439 99.97 0.21216 0.20949 0.205 0.26859 0.2645 RANDOM 16.542
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.676 r_dihedral_angle_4_deg 25.588 r_dihedral_angle_3_deg 19.933 r_dihedral_angle_1_deg 7.65 r_scangle_it 2.881 r_scbond_it 1.852 r_angle_refined_deg 1.744 r_mcangle_it 1.064 r_mcbond_it 0.628 r_nbtor_refined 0.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.676 r_dihedral_angle_4_deg 25.588 r_dihedral_angle_3_deg 19.933 r_dihedral_angle_1_deg 7.65 r_scangle_it 2.881 r_scbond_it 1.852 r_angle_refined_deg 1.744 r_mcangle_it 1.064 r_mcbond_it 0.628 r_nbtor_refined 0.329 r_nbd_refined 0.226 r_symmetry_vdw_refined 0.195 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.115 r_symmetry_hbond_refined 0.107 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 1629 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 73
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction