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Crystal structure of the IIBSor domain of the sorbose permease from Klebsiella pneumoniae solved to 1.75A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BLE PDB ENTRY 1BLE cut down to common atoms
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 19-25% PEG 8000, 0.2M ammonium sulphate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.32 46.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.848 α = 90 b = 85.311 β = 103.02 c = 67.815 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 IMAGE PLATE MARRESEARCH MIRRORS 2001-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ELLIOTT GX-20 1.5418
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 1.75 21.38 99.6 0.051 0.051 9.5 2.5 72155 72155 20.16
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 1.75 1.84 99.8 0.235 0.235 3.1 2.4 15789
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 1BLE cut down to common atoms 1.75 21.37 68518 3637 99.65 0.21731 0.21593 0.2253 0.24268 0.2532 RANDOM 8.907
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] 1.9 0.83 -0.95 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.64 r_dihedral_angle_1_deg 3.996 r_scangle_it 2.769 r_scbond_it 1.648 r_angle_refined_deg 1.346 r_mcangle_it 0.928 r_angle_other_deg 0.722 r_mcbond_it 0.486 r_symmetry_hbond_refined 0.364 r_symmetry_vdw_other 0.362
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.64 r_dihedral_angle_1_deg 3.996 r_scangle_it 2.769 r_scbond_it 1.648 r_angle_refined_deg 1.346 r_mcangle_it 0.928 r_angle_other_deg 0.722 r_mcbond_it 0.486 r_symmetry_hbond_refined 0.364 r_symmetry_vdw_other 0.362 r_symmetry_vdw_refined 0.303 r_nbd_refined 0.238 r_nbd_other 0.202 r_xyhbond_nbd_refined 0.18 r_xyhbond_nbd_other 0.087 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5148 Nucleic Acid Atoms Solvent Atoms 468 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing