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Crystal structure of unknown conserved ybaA protein from Shigella flexneri
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 0.5M Sodium chloride, 1.6M Sodium citrate tribasic dihydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.04 39.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.843 α = 90 b = 61.843 β = 90 c = 137.32 γ = 90
Symmetry Space Group P 41 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 mirrors 2006-10-29 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARRESEARCH mirrors 2006-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97857 APS 23-ID-B 2 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97869 APS 21-ID-D
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 1.8 25 99.7 0.045 36.1 6.1 25474 25474 -3
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) 1.8 1.86 99.1 0.254 5.3 4.9 2467
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.8 20.39 24161 1255 99.79 0.18494 0.1828 0.1837 0.22635 0.2273 RANDOM 27.991
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] 0.84 0.84 -1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.551 r_dihedral_angle_4_deg 20.992 r_dihedral_angle_3_deg 13.977 r_dihedral_angle_1_deg 6.521 r_scangle_it 4.286 r_scbond_it 2.611 r_mcangle_it 2.042 r_angle_refined_deg 1.279 r_mcbond_it 1.156 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.551 r_dihedral_angle_4_deg 20.992 r_dihedral_angle_3_deg 13.977 r_dihedral_angle_1_deg 6.521 r_scangle_it 4.286 r_scbond_it 2.611 r_mcangle_it 2.042 r_angle_refined_deg 1.279 r_mcbond_it 1.156 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.212 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.163 r_metal_ion_refined 0.163 r_chiral_restr 0.104 r_symmetry_metal_ion_refined 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2097 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling SHARP phasing