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Crystal structure of RseB: a sensor for periplasmic stress response in E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other LARGE DOMAIN FROM P4212 DATASET
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 PROTEIN WAS CRYSTALLIZED FROM 0.2 M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1 M TRIS-HCL PH 8.5, 25%(W/V) POLYETHYLENE GLYCOL 3350 AND 10 MM L-CYSTEINE
Crystal Properties Matthews coefficient Solvent content 2.66 53.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.6 α = 90 b = 200.7 β = 90 c = 109.73 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 CCD 2005-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.4 20 95.2 0.11 12.6 3.7 40893 2.4
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 2.37 2.5 89.4 0.58 2.4 3.8
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 LARGE DOMAIN FROM P4212 DATASET 2.37 20 41422 2205 98.5 0.231 0.228 0.2196 0.278 0.2674 RANDOM 49.48
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] -1.06 1.73 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.188 r_dihedral_angle_1_deg 20.178 r_dihedral_angle_3_deg 19.193 r_dihedral_angle_4_deg 17.841 r_scangle_it 2.038 r_angle_refined_deg 1.697 r_scbond_it 1.246 r_mcangle_it 0.953 r_mcbond_it 0.549 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.188 r_dihedral_angle_1_deg 20.178 r_dihedral_angle_3_deg 19.193 r_dihedral_angle_4_deg 17.841 r_scangle_it 2.038 r_angle_refined_deg 1.697 r_scbond_it 1.246 r_mcangle_it 0.953 r_mcbond_it 0.549 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.254 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.199 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.12 r_bond_refined_d 0.011 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_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 6456 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling