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Crystal structure of a tautomerase superfamily member form Acinetobacter baumanii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LKB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 296 1 ul protein (20 mM HEPES-NaOH pH 6.8, 150 mM NaCl) mixed with 1 ul of reservoir solution (0.2 M NH4NO3 and 20% w/v PEG3350)
Crystal Properties Matthews coefficient Solvent content 2.15 42.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.185 α = 90 b = 59.185 β = 90 c = 97.757 γ = 120
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 RIGAKU SATURN 944 2020-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.7 45.394 97.3 0.044 0.051 0.023 0.999 4.1 7 13698
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 87 0.951
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 4LKB 1.7 45.39 13022 675 97.28 0.1394 0.137 0.1518 0.1863 0.1925 RANDOM 13.072
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] 0.14 0.07 0.14 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.693 r_dihedral_angle_4_deg 15.82 r_dihedral_angle_3_deg 14.386 r_dihedral_angle_1_deg 6.626 r_angle_refined_deg 1.969 r_angle_other_deg 1.039 r_chiral_restr 0.121 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.693 r_dihedral_angle_4_deg 15.82 r_dihedral_angle_3_deg 14.386 r_dihedral_angle_1_deg 6.626 r_angle_refined_deg 1.969 r_angle_other_deg 1.039 r_chiral_restr 0.121 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1011 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing