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Crystal structure of E. coli ApaH D37A mutant in complex with Ap4U
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DFJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 Conditions: 0.3 mM ApaH (D37A) mutant (10 mg/mL), 1 mM DTT, 25 mM Hepes (pH 7.5), 0.2 M NaCl and soaked with Ap4U.
Well solution: 0.2 M Trisodium Citrate, 20% PEG3350.
Crystal Properties Matthews coefficient Solvent content 3.52 65.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.055 α = 90 b = 55.033 β = 129.58 c = 119.751 γ = 90
Symmetry Space Group C 1 2 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 9M 2023-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92010 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.82 32.2 99.7 0.184 0.988 5.2 4.7 74138 25.15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.86 100 1.735 0.355 0.9 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.83 32.2 1.34 73812 3693 99.29 0.1923 0.1908 0.1904 0.2218 0.2208
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 f_dihedral_angle_d 8.539 f_angle_d 1.052 f_chiral_restr 0.056 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4199 Nucleic Acid Atoms Solvent Atoms 565 Heterogen Atoms 71
Software Software Software Name Purpose PHENIX refinement autoPROC data scaling autoPROC data reduction Coot model building PHASER phasing