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Crystal structure of IpgB2 from Shigella flexneri
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 277 5% (w/w) PEG 3350, 7% isopropanol, 10mM FeCl3, 100mM trisodium citrate/citric acid pH 5.5, 10mM NaCl, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.29 62.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.08 α = 90 b = 114.08 β = 90 c = 88.77 γ = 90
Symmetry Space Group P 4 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 100 CCD MARRESEARCH 2008-09-21 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARRESEARCH 2009-11-25 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.900 ESRF ID23-1 2 SYNCHROTRON ESRF BEAMLINE ID23-1 0.979 ESRF ID23-1
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 1,2 2.3 22.88 95.4 0.056 33.35 18.2 25363 -3 49.2
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) 1,2 2.3 2.36 63 0.675 2.6 6.4 1205
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 SAD THROUGHOUT 2.3 22.88 -3 24089 1267 95.6 0.232 0.229 0.2284 0.292 0.2923 RANDOM 45.838
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] -0.34 -0.34 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.742 r_dihedral_angle_4_deg 19.853 r_dihedral_angle_3_deg 19.363 r_dihedral_angle_1_deg 5.612 r_scangle_it 3.825 r_scbond_it 2.249 r_angle_refined_deg 1.694 r_mcangle_it 1.576 r_mcbond_it 0.825 r_chiral_restr 0.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.742 r_dihedral_angle_4_deg 19.853 r_dihedral_angle_3_deg 19.363 r_dihedral_angle_1_deg 5.612 r_scangle_it 3.825 r_scbond_it 2.249 r_angle_refined_deg 1.694 r_mcangle_it 1.576 r_mcbond_it 0.825 r_chiral_restr 0.164 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2957 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 45
Software Software Software Name Purpose XSCALE data scaling SHELX phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection XDS data reduction SHELXD phasing