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CRYSTAL STRUCTURE OF E. COLI K-12 YGGS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B54 PDB ENTRY 1B54
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 20% PEG 4000, 16% ISOPROPANOL, 0.1 M NA-CITRATE BUFFER PH 6, 5% SODIUM DEXTRANE SULPHATE
Crystal Properties Matthews coefficient Solvent content 3.1 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.017 α = 90 b = 124.017 β = 90 c = 83.729 γ = 90
Symmetry Space Group I 41 2 2
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 CCD 2003-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 39 99.9 0.05 0.05 34.2 9 22295 25.32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 100 0.34 0.34 5.9 9.1
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 PDB ENTRY 1B54 2 39 21064 1222 100 0.163 0.161 0.1749 0.195 0.2022 RANDOM 21.57
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] 0.28 0.28 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.179 r_dihedral_angle_4_deg 18.107 r_dihedral_angle_3_deg 14.153 r_dihedral_angle_1_deg 5.261 r_scangle_it 2.337 r_scbond_it 1.557 r_angle_refined_deg 1.119 r_mcangle_it 0.876 r_mcbond_it 0.819 r_angle_other_deg 0.774
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.179 r_dihedral_angle_4_deg 18.107 r_dihedral_angle_3_deg 14.153 r_dihedral_angle_1_deg 5.261 r_scangle_it 2.337 r_scbond_it 1.557 r_angle_refined_deg 1.119 r_mcangle_it 0.876 r_mcbond_it 0.819 r_angle_other_deg 0.774 r_symmetry_vdw_other 0.236 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.197 r_symmetry_vdw_refined 0.187 r_nbd_other 0.186 r_xyhbond_nbd_refined 0.173 r_nbtor_refined 0.166 r_nbtor_other 0.082 r_chiral_restr 0.062 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1740 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALA data scaling AMoRE phasing