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Crystal Structure of Protein of Unknown Function YfiH from Shigella flexneri 2a str. 2457T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 PEG 3350, Zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.2 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.874 α = 90.32 b = 50.583 β = 96.32 c = 55.347 γ = 90.4
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 SBC-2 mirrors 2004-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9793 APS 19-ID
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 2.01 55.05 97.4 0.071 11.3 4.7 31355 30856
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 2.01 2.08 89.6 0.206 6.5 3.9 2849
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.01 55.05 27582 27582 3071 96.91 0.18583 0.18583 0.1786 0.178 0.25159 0.2514 RANDOM 22.5
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] 0.98 -0.07 -0.81 -0.79 0.03 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.409 r_dihedral_angle_4_deg 19.485 r_dihedral_angle_3_deg 16.65 r_dihedral_angle_1_deg 6.668 r_scangle_it 3.619 r_scbond_it 2.617 r_angle_refined_deg 1.517 r_mcangle_it 1.505 r_mcbond_it 1.061 r_symmetry_vdw_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.409 r_dihedral_angle_4_deg 19.485 r_dihedral_angle_3_deg 16.65 r_dihedral_angle_1_deg 6.668 r_scangle_it 3.619 r_scbond_it 2.617 r_angle_refined_deg 1.517 r_mcangle_it 1.505 r_mcbond_it 1.061 r_symmetry_vdw_refined 0.302 r_xyhbond_nbd_refined 0.223 r_nbd_refined 0.216 r_symmetry_hbond_refined 0.208 r_chiral_restr 0.103 r_metal_ion_refined 0.028 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_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 3688 Nucleic Acid Atoms Solvent Atoms 420 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data scaling HKL-3000 phasing