☰ Navigation Tabs
Crystal Structure of the N-terminal N-formyltransferase Domain (residues 1-306) of Escherichia coli Arna in Complex with UDP-Ara4N and Folinic Acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BLN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 294 20 to 22% poly(ethylene glycol) 5000, 50 mM MgCl2, 5 mM N5-formyltetrahydrofolate, 10 mM UDP-Ara4N, and 100 mM HEPPS (pH 8.0)
Crystal Properties Matthews coefficient Solvent content 2.87 57.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.994 α = 89.94 b = 76.206 β = 63.78 c = 84.852 γ = 61.54
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 ADSC QUANTUM 210r 2015-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.99768 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.5 20 91.3 0.056 0.056 28.5 2.5 45712
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.55 88.7 0.144 11.8 2.2
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 2BLN 2.5 20 43477 2253 91.25 0.21571 0.21213 0.22 0.28404 0.2891 RANDOM 34.422
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] 1.84 -1.35 1.28 1.31 0.18 -2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.602 r_dihedral_angle_4_deg 19.356 r_dihedral_angle_3_deg 16.398 r_dihedral_angle_1_deg 7.29 r_long_range_B_refined 5.525 r_long_range_B_other 5.493 r_mcangle_it 3.474 r_mcangle_other 3.474 r_scangle_other 3.435 r_mcbond_it 2.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.602 r_dihedral_angle_4_deg 19.356 r_dihedral_angle_3_deg 16.398 r_dihedral_angle_1_deg 7.29 r_long_range_B_refined 5.525 r_long_range_B_other 5.493 r_mcangle_it 3.474 r_mcangle_other 3.474 r_scangle_other 3.435 r_mcbond_it 2.164 r_mcbond_other 2.163 r_scbond_it 2.069 r_scbond_other 2.069 r_angle_refined_deg 1.685 r_angle_other_deg 0.991 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 9145 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 228
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing