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Structural Insights into the Mechanism of Escherichia coli Ymdb
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SPV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 285 0.2 M potassium sodium tartrate tetrahydrate, 20%(w/v) polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.19 43.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.902 α = 90 b = 42.059 β = 103.23 c = 70.346 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 CCD ADSC QUANTUM 315r 2014-01-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9791 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 50 99 0.064 37 4.2 15827
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 1.8 1.83 99.4 0.256 7.3 4.3
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 1SPV 1.8 29.04 15038 791 98.88 0.1893 0.1878 0.1964 0.21726 0.228 RANDOM 26.363
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] -0.6 -0.27 0.61 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.445 r_dihedral_angle_4_deg 24.921 r_dihedral_angle_3_deg 16.758 r_dihedral_angle_1_deg 5.288 r_long_range_B_refined 4.261 r_long_range_B_other 3.931 r_scangle_other 2.012 r_mcangle_it 1.747 r_mcangle_other 1.746 r_angle_refined_deg 1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.445 r_dihedral_angle_4_deg 24.921 r_dihedral_angle_3_deg 16.758 r_dihedral_angle_1_deg 5.288 r_long_range_B_refined 4.261 r_long_range_B_other 3.931 r_scangle_other 2.012 r_mcangle_it 1.747 r_mcangle_other 1.746 r_angle_refined_deg 1.38 r_scbond_it 1.312 r_scbond_other 1.31 r_mcbond_other 0.992 r_mcbond_it 0.991 r_angle_other_deg 0.807 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_bond_other_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 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 1253 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement Coot model building HKL-2000 data processing