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Crystal Structure of domain-swapped Circular-Permuted YbeA (CP74) from Escherichia coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293.15 25% PEG 8000, 0.1M PIPES 2 VAPOR DIFFUSION, SITTING DROP 7 293.15 25% PEG 8000, 0.1M PIPES
Crystal Properties Matthews coefficient Solvent content 2.36 47.79 2.36 47.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.458 α = 90 b = 88.053 β = 101.47 c = 81.184 γ = 90
Symmetry Space Group P 1 21 1
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 RAYONIX MX300HE 2018-03-12 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD ADSC QUANTUM 315r 2017-12-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.00928 NSRRC BL15A1 2 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0000 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.75 30 99.5 0.033 0.039 0.02 34.82 3.7 65452
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81 98.1 0.439 0.525 0.285 0.824 2.13 3.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.75 29.52 62103 3326 99.25 0.1706 0.16933 0.19466 0.203 RANDOM 43.475
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] 0.74 -0.3 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.805 r_dihedral_angle_3_deg 16.909 r_dihedral_angle_4_deg 16.718 r_long_range_B_refined 8.586 r_scbond_it 7.084 r_mcangle_it 6.658 r_dihedral_angle_1_deg 5.712 r_mcbond_it 5.478 r_rigid_bond_restr 4.087 r_angle_refined_deg 1.381
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.805 r_dihedral_angle_3_deg 16.909 r_dihedral_angle_4_deg 16.718 r_long_range_B_refined 8.586 r_scbond_it 7.084 r_mcangle_it 6.658 r_dihedral_angle_1_deg 5.712 r_mcbond_it 5.478 r_rigid_bond_restr 4.087 r_angle_refined_deg 1.381 r_chiral_restr 0.102 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4704 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data scaling HKL-2000 data reduction PHENIX phasing