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Crystal structure of the C-terminal domain of the yjiK protein from Escherichia coli CFT073
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M sodium Cacodylate, 0.2 M Calcium Acetate, 40% Peg 300, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.2 61.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.024 α = 90 b = 130.024 β = 90 c = 130.024 γ = 90
Symmetry Space Group P 41 3 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 ADSC QUANTUM 315r mirrors 2010-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 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 2.55 40 100 0.084 37 11.6 12816 12816 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 2.55 40 2 2 12698 12078 620 99.38 0.232 0.23179 0.22891 0.2272 0.29067 0.2811 RANDOM 39.673
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.642 r_dihedral_angle_4_deg 25.91 r_dihedral_angle_3_deg 17.498 r_dihedral_angle_1_deg 7.669 r_scangle_it 3.903 r_scbond_it 2.442 r_angle_refined_deg 1.636 r_mcangle_it 1.622 r_angle_other_deg 0.931 r_mcbond_it 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.642 r_dihedral_angle_4_deg 25.91 r_dihedral_angle_3_deg 17.498 r_dihedral_angle_1_deg 7.669 r_scangle_it 3.903 r_scbond_it 2.442 r_angle_refined_deg 1.636 r_mcangle_it 1.622 r_angle_other_deg 0.931 r_mcbond_it 0.85 r_mcbond_other 0.157 r_chiral_restr 0.102 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1867 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 4
Software Software Software Name Purpose SBC-Collect data collection PHENIX model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing