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The evolving story of AtzT, a periplasmic binding protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Protein at 20 mg/mL in SD2 plates incubated at 20 C. Conditions contained 6-8% Jeffamine M600 with 2-7% MPD and trisodium citrate at 1.1-1.2 M
Crystal Properties Matthews coefficient Solvent content 2.58 52.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.92 α = 90 b = 63.05 β = 93.49 c = 120.436 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 PIXEL DECTRIS EIGER X 16M 2018-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 1.008020 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.87 49.4 97.8 0.14 0.032 0.998 13.5 19.6 119947
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.9 80.1 0.669 0.246 0.809 3.1 7.4
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 1.87 49.4 114140 5791 97.59 0.15624 0.15486 0.1697 0.18303 0.1938 RANDOM 32.759
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] 1.68 2.47 -2 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.018 r_dihedral_angle_3_deg 14.805 r_dihedral_angle_4_deg 11.229 r_long_range_B_refined 7.089 r_long_range_B_other 7.076 r_scangle_other 6.599 r_dihedral_angle_1_deg 5.822 r_scbond_it 4.435 r_scbond_other 4.405 r_mcangle_it 3.698
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.018 r_dihedral_angle_3_deg 14.805 r_dihedral_angle_4_deg 11.229 r_long_range_B_refined 7.089 r_long_range_B_other 7.076 r_scangle_other 6.599 r_dihedral_angle_1_deg 5.822 r_scbond_it 4.435 r_scbond_other 4.405 r_mcangle_it 3.698 r_mcangle_other 3.697 r_mcbond_it 2.872 r_mcbond_other 2.871 r_angle_refined_deg 1.548 r_angle_other_deg 1.412 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10065 Nucleic Acid Atoms Solvent Atoms 648 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement ADDREF data reduction Aimless data scaling CRANK2 phasing