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ABC transporter binding protein CebE from Streptomyces scabiei in complex with cellotriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold alphafold model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 277 PEG3350 25%, sodium citrate pH 3.5 100mM
Crystal Properties Matthews coefficient Solvent content 2.05 39.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.39 α = 90 b = 39.43 β = 92.38 c = 79.64 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 PIXEL DECTRIS PILATUS3 6M 2014-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9786 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.55 35.33 99.2 0.084 0.999 13.15 3.8 53542
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.59 97.1 1.333 0.524 3.14
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE alphafold model 1.55 35.33 53542 2678 99.227 0.138 0.1357 0.1324 0.1776 0.1773 24.808
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] -0.762 -0.407 -0.977 1.766
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.218 r_dihedral_angle_3_deg 14.021 r_dihedral_angle_2_deg 11.125 r_dihedral_angle_1_deg 6.358 r_lrange_it 3.15 r_rigid_bond_restr 3.133 r_lrange_other 2.742 r_scangle_it 1.969 r_scangle_other 1.969 r_mcangle_it 1.712
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.218 r_dihedral_angle_3_deg 14.021 r_dihedral_angle_2_deg 11.125 r_dihedral_angle_1_deg 6.358 r_lrange_it 3.15 r_rigid_bond_restr 3.133 r_lrange_other 2.742 r_scangle_it 1.969 r_scangle_other 1.969 r_mcangle_it 1.712 r_mcangle_other 1.712 r_scbond_it 1.452 r_scbond_other 1.451 r_angle_refined_deg 1.373 r_mcbond_it 1.251 r_mcbond_other 1.23 r_angle_other_deg 0.458 r_symmetry_xyhbond_nbd_refined 0.239 r_nbd_refined 0.221 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.15 r_nbd_other 0.14 r_symmetry_nbd_refined 0.132 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2974 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing