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Crystal structure of Staphylococcal Superantigen-Like protein 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RDH PDB ENTRIES 2RDH and 2Z8L experimental model PDB 2Z8L PDB ENTRIES 2RDH and 2Z8L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291.15 21% MPEG 5000, 0.2M bis-tris propane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Crystal Properties Matthews coefficient Solvent content 2.3 46.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.102 α = 90 b = 81.195 β = 105.45 c = 57.301 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 100 IMAGE PLATE MAR scanner 345 mm plate Osmic mirrors 2010-05-05 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 1.7 27.62 99.7 0.058 17.14 9.9 46435 28.8
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 1.78 99.2 0.698 9.6 6696
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 ENTRIES 2RDH and 2Z8L 1.7 27.62 44078 2345 99.55 0.21126 0.20864 0.2016 0.2614 0.2501 RANDOM 29.686
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] -1.98 -1.72 0.91 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.412 r_dihedral_angle_4_deg 20.408 r_dihedral_angle_3_deg 14.348 r_dihedral_angle_1_deg 5.9 r_scangle_it 5.554 r_scbond_it 3.423 r_mcangle_it 2.353 r_angle_refined_deg 2.096 r_mcbond_it 1.407 r_chiral_restr 0.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.412 r_dihedral_angle_4_deg 20.408 r_dihedral_angle_3_deg 14.348 r_dihedral_angle_1_deg 5.9 r_scangle_it 5.554 r_scbond_it 3.423 r_mcangle_it 2.353 r_angle_refined_deg 2.096 r_mcbond_it 1.407 r_chiral_restr 0.157 r_bond_refined_d 0.025 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 3108 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 10
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling