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Structure and Function of the E. coli Protein YmgB: a Protein Critical for Biofilm Formation and Acid Resistance
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8 295 90 mM Tris, 1.8 M NaCl, 0.5 (w/v)% B-OG, pH 8.0, microbatch, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.45 49.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.919 α = 90 b = 69.945 β = 90 c = 55.021 γ = 90
Symmetry Space Group C 2 2 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 CCD ADSC QUANTUM 210 Toroidal focusing mirror 2006-10-25 M MAD 2 1 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.9790, 0.9793, 0.9322 NSLS X6A
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 45 99.6 0.038 22.8 6.6 12849 12802 1 1
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 1.86 96.8 0.403 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.8 20 12849 12174 625 99.67 0.21567 0.21456 0.23789 0.2234 RANDOM 20.249
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] 0.24 0.17 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.36 r_dihedral_angle_4_deg 21.786 r_dihedral_angle_3_deg 12.009 r_scangle_it 9.083 r_scbond_it 6.463 r_dihedral_angle_1_deg 3.992 r_mcangle_it 3.5 r_mcbond_it 2.539 r_angle_refined_deg 1.666 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.36 r_dihedral_angle_4_deg 21.786 r_dihedral_angle_3_deg 12.009 r_scangle_it 9.083 r_scbond_it 6.463 r_dihedral_angle_1_deg 3.992 r_mcangle_it 3.5 r_mcbond_it 2.539 r_angle_refined_deg 1.666 r_nbtor_refined 0.296 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.11 r_chiral_restr 0.087 r_symmetry_hbond_refined 0.057 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 954 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 40
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling