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Crystal structure of the E. coli maltodextrin-binding protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MPB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.1 M Tris pH 7.4, 30 % PEG Smear
Broad, 0.1 M NaBr and 0.1 M KSCN
Crystal Properties Matthews coefficient Solvent content 1.95 36.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.709 α = 90 b = 64.961 β = 101.05 c = 57.09 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 PILATUS 2M-F 2020-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.15 56.04 99.5 0.999 13.3 6.4 110383
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.17 0.799
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.15 37.76 104767 5585 99.41 0.12498 0.12355 0.1236 0.15203 0.1518 RANDOM 10.422
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] -0.08 -0.12 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.471 r_dihedral_angle_4_deg 15.811 r_dihedral_angle_3_deg 13.624 r_dihedral_angle_1_deg 5.793 r_rigid_bond_restr 3.57 r_long_range_B_refined 3.243 r_long_range_B_other 3.086 r_scangle_other 3.064 r_scbond_other 2.617 r_scbond_it 2.608
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.471 r_dihedral_angle_4_deg 15.811 r_dihedral_angle_3_deg 13.624 r_dihedral_angle_1_deg 5.793 r_rigid_bond_restr 3.57 r_long_range_B_refined 3.243 r_long_range_B_other 3.086 r_scangle_other 3.064 r_scbond_other 2.617 r_scbond_it 2.608 r_mcangle_other 2.533 r_mcangle_it 2.532 r_mcbond_it 1.986 r_mcbond_other 1.984 r_angle_refined_deg 1.983 r_angle_other_deg 1.67 r_chiral_restr 0.129 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2853 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing