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High resolution structure of E. coli glucose/galactose binding protein bound with glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GBP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 290 20% PEG6000, 50mM NaHEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.02 39.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.26 α = 90 b = 36.58 β = 107.19 c = 64.94 γ = 90
Symmetry Space Group P 1 21 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 MAR CCD 165 mm 2003-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.90 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 1.33 25 98.3 0.161 5.22 62566 62566 -3 14.341
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) 1.33 1.5 94.9 89.2 0.343 3.18 18133
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2GBP 1.33 24.57 62566 62564 3129 100 0.155 0.155 0.154 0.1624 0.178 0.1848 RANDOM 6.717
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] -0.01 0.12 0.44 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.852 r_dihedral_angle_3_deg 11.546 r_dihedral_angle_4_deg 10.104 r_dihedral_angle_1_deg 5.468 r_sphericity_free 4.482 r_scangle_it 3.059 r_scbond_it 2.185 r_sphericity_bonded 1.984 r_mcangle_it 1.437 r_angle_refined_deg 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.852 r_dihedral_angle_3_deg 11.546 r_dihedral_angle_4_deg 10.104 r_dihedral_angle_1_deg 5.468 r_sphericity_free 4.482 r_scangle_it 3.059 r_scbond_it 2.185 r_sphericity_bonded 1.984 r_mcangle_it 1.437 r_angle_refined_deg 1.3 r_mcbond_it 1.083 r_rigid_bond_restr 1.001 r_angle_other_deg 0.881 r_mcbond_other 0.385 r_symmetry_vdw_refined 0.286 r_nbd_refined 0.225 r_nbd_other 0.18 r_nbtor_refined 0.175 r_symmetry_vdw_other 0.169 r_xyhbond_nbd_refined 0.122 r_symmetry_hbond_refined 0.113 r_nbtor_other 0.085 r_chiral_restr 0.083 r_metal_ion_refined 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2388 Nucleic Acid Atoms Solvent Atoms 523 Heterogen Atoms 13
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction AMoRE phasing