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Rational stabilization of E. coli ribose binding protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DRI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 290 36% PEG4000, 0.1M NaAcetate pH5.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.08 40.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.847 α = 90 b = 71.05 β = 90 c = 98.949 γ = 90
Symmetry Space Group P 21 21 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 MAR CCD 165 mm 2003-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 1.9 50 99.6 0.161 5.2 6.7 20182 20182
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 1.9 1.97 96.6 0.858 1.9 6.2 1913
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2DRI 1.97 50 3.1 18058 18058 925 99.95 0.182 0.182 0.179 0.1856 0.229 0.2285 RANDOM 14.801
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] 0.25 0.36 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.801 r_dihedral_angle_4_deg 22.569 r_dihedral_angle_3_deg 13.05 r_dihedral_angle_1_deg 5.816 r_scangle_it 3.173 r_scbond_it 2.225 r_angle_refined_deg 1.344 r_mcangle_it 1.131 r_mcbond_it 0.981 r_angle_other_deg 0.918
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.801 r_dihedral_angle_4_deg 22.569 r_dihedral_angle_3_deg 13.05 r_dihedral_angle_1_deg 5.816 r_scangle_it 3.173 r_scbond_it 2.225 r_angle_refined_deg 1.344 r_mcangle_it 1.131 r_mcbond_it 0.981 r_angle_other_deg 0.918 r_symmetry_vdw_other 0.22 r_symmetry_vdw_refined 0.201 r_nbd_refined 0.199 r_nbd_other 0.186 r_xyhbond_nbd_refined 0.175 r_symmetry_hbond_refined 0.175 r_nbtor_refined 0.16 r_mcbond_other 0.159 r_nbtor_other 0.085 r_chiral_restr 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2001 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection AMoRE phasing