☰ Navigation Tabs
Joint Xray/Neutron structure of Escherichia coli YajL at room temperature
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AB0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 100 mM Tris pH=8.0, 250 mM MgCl2 and 20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.09 41.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.289 α = 90 b = 79.303 β = 90 c = 100.183 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS EIGER2 R 4M 2021-09-20 M SINGLE WAVELENGTH 2 1 neutron 293 SCINTILLATION ORNL ANGER CAMERA 2021-09-07 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.542 2 SPALLATION SOURCE ORNL Spallation Neutron Source BEAMLINE MANDI 2.00-4.16 ORNL Spallation Neutron Source MANDI
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (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 1.65 100.18 99.7 0.995 26.96 8.9 43186 15.91 2 1.79 14.61 97.1 0.905 12.7 6.9 32647 15.91
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.71 0.738 2 1.79 1.86 0.604
Refinement Statistics Diffraction ID Structure Solution 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 MOLECULAR REPLACEMENT 1.65 25.56 1.34 43084 2215 99.64 0.1385 0.1371 0.1368 0.1642 0.1634 25.26 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 1.79 14.6 32639 96.73 0.1774 0.2226
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 16.752 f_dihedral_angle_d 16.752 f_angle_d 1.223 f_angle_d 1.223 f_chiral_restr 0.072 f_chiral_restr 0.072 f_bond_d 0.009 f_bond_d 0.009 f_plane_restr 0.007 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2902 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement