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Atomic resolution structure of reduced E. coli YajL
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 8.5 298 polyethylene glycol 4000, Tris HCl, magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.03 39.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.875 α = 90 b = 78.313 β = 90 c = 99.434 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 100 PIXEL DECTRIS PILATUS 6M Rh coated collimating mirrors, K-B focusing mirrors 2015-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.73 SSRL BL12-2
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 0.98 38 97.6 0.085 1 15.9 10.2 191363
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 0.98 1 96 2.393 0.479 1.1 9.5
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 2AB0 0.98 61.52 187313 3842 97.34 0.11427 0.11403 0.1134 0.1266 0.1264 RANDOM 12.354
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] 0.03 -0.1 0.06
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.477 r_dihedral_angle_2_deg 33.298 r_dihedral_angle_4_deg 14.352 r_dihedral_angle_3_deg 10.834 r_sphericity_bonded 8.706 r_dihedral_angle_1_deg 6.254 r_rigid_bond_restr 3.449 r_long_range_B_refined 3.171 r_long_range_B_other 2.487 r_scangle_other 2.119
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.477 r_dihedral_angle_2_deg 33.298 r_dihedral_angle_4_deg 14.352 r_dihedral_angle_3_deg 10.834 r_sphericity_bonded 8.706 r_dihedral_angle_1_deg 6.254 r_rigid_bond_restr 3.449 r_long_range_B_refined 3.171 r_long_range_B_other 2.487 r_scangle_other 2.119 r_angle_refined_deg 1.937 r_scbond_it 1.797 r_scbond_other 1.745 r_mcangle_other 1.449 r_mcangle_it 1.448 r_angle_other_deg 1.183 r_mcbond_it 1.059 r_mcbond_other 1.049 r_chiral_restr 0.164 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2902 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing