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The Crystal structure of Delta protein of pSM19035 from Streptoccocus pyogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BEJ PDB entry 2Bej
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.9M Na-Hepes, 2% Ethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.37 63.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.968 α = 90 b = 82.968 β = 90 c = 233.998 γ = 120
Symmetry Space Group P 65 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 MARRESEARCH 2004-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.972 BESSY 14.1
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 1.83 50 99.9 0.062 11.8 9.2 43046 43046 26.2
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) 1.83 1.87 99.9 0.396 3.9 8.1 42966
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-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 2Bej 1.83 28.5 42966 40877 2054 99.57 0.19235 0.1933 0.21804 0.1938 RANDOM 26.436
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] 0.25 0.13 0.25 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.837 r_dihedral_angle_3_deg 12.932 r_dihedral_angle_4_deg 12.918 r_rigid_bond_restr 7.028 r_dihedral_angle_1_deg 5.638 r_sphericity_free 4.691 r_sphericity_bonded 4.021 r_scangle_it 3.85 r_scbond_it 2.391 r_mcangle_it 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.837 r_dihedral_angle_3_deg 12.932 r_dihedral_angle_4_deg 12.918 r_rigid_bond_restr 7.028 r_dihedral_angle_1_deg 5.638 r_sphericity_free 4.691 r_sphericity_bonded 4.021 r_scangle_it 3.85 r_scbond_it 2.391 r_mcangle_it 1.51 r_angle_refined_deg 1.34 r_mcbond_it 0.945 r_nbtor_refined 0.308 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.165 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.096 r_symmetry_hbond_refined 0.079 r_metal_ion_refined 0.049 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2312 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling PHASER phasing