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Crystal Structure of the Staphylococcal superantigen-like protein SSL5 at pH 4.6 complexed 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 4.6 291 20% PEG 3350, 0.2M NaH2PO4, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.65 53.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.625 α = 90 b = 78.237 β = 127.02 c = 55.276 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 110 CCD MARMOSAIC 325 mm CCD mirror, monochromator 2006-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97892 SSRL BL9-2
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 1.65 30.04 99.8 0.051 25.6 7.4 30728 30702
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 1.65 1.74 100 0.667 2.5 7.4 4497
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1M4V 1.65 28.05 30790 30702 1538 99.81 0.183 0.183 0.181 0.218 0.2781 RANDOM 16.92
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] 0.31 0.37 -0.22 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.736 r_dihedral_angle_4_deg 15.319 r_dihedral_angle_3_deg 13.459 r_dihedral_angle_1_deg 6.175 r_scangle_it 4.532 r_scbond_it 3.517 r_mcangle_it 2.093 r_mcbond_it 1.866 r_angle_refined_deg 1.744 r_angle_other_deg 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.736 r_dihedral_angle_4_deg 15.319 r_dihedral_angle_3_deg 13.459 r_dihedral_angle_1_deg 6.175 r_scangle_it 4.532 r_scbond_it 3.517 r_mcangle_it 2.093 r_mcbond_it 1.866 r_angle_refined_deg 1.744 r_angle_other_deg 0.91 r_mcbond_other 0.358 r_symmetry_vdw_other 0.236 r_nbd_refined 0.21 r_nbd_other 0.194 r_nbtor_refined 0.188 r_symmetry_vdw_refined 0.166 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.143 r_chiral_restr 0.115 r_nbtor_other 0.094 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1607 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 67
Software Software Software Name Purpose MOSFLM data reduction PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection SCALA data scaling