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Crystal structure of Staphylococcal Superantigen-Like protein 11 in complex with Sialyl Lewis X
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 291 20% PEG3350, 0.2M potassium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.64 53.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.031 α = 90 b = 57.945 β = 101.83 c = 43.462 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 IMAGE PLATE RIGAKU RAXIS IV 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) 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 1.6 30.7 91.5 0.054 7.2 28611
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 1.6 1.69 80.1 0.114 10.1 7.1 3623
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 1.6 22.45 28588 1430 91.63 0.17576 0.17417 0.172 0.20656 0.2044 RANDOM 23.827
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 -0.03 -0.03 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.395 r_dihedral_angle_4_deg 13.582 r_dihedral_angle_3_deg 11.122 r_dihedral_angle_1_deg 5.904 r_scangle_it 2.726 r_scbond_it 1.734 r_angle_refined_deg 1.21 r_mcangle_it 1.003 r_mcbond_it 0.549 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.395 r_dihedral_angle_4_deg 13.582 r_dihedral_angle_3_deg 11.122 r_dihedral_angle_1_deg 5.904 r_scangle_it 2.726 r_scbond_it 1.734 r_angle_refined_deg 1.21 r_mcangle_it 1.003 r_mcbond_it 0.549 r_nbtor_refined 0.306 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.192 r_symmetry_vdw_refined 0.152 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.084 r_metal_ion_refined 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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_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 1553 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing