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A molecular switch changes the low to the high affinity state in the substrate binding protein AfProX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SW5 PDB entry 1SW5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 100 mM HEPES, 15-25% PEG6000, 15-25% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.3 46.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.792 α = 96.07 b = 36.958 β = 99.57 c = 57.886 γ = 96.12
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 73 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.8 20 95 0.039 27.9 4.2 25271 22833 24.6
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 1.8 2 95.1 0.114 12.08 4.3 6780
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 1SW5 1.8 19.99 21690 1142 100 0.20407 0.20176 0.2003 0.24681 0.2445 RANDOM 20.035
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] 0.32 1.01 0.43 0.37 0.42 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.092 r_dihedral_angle_3_deg 14.261 r_dihedral_angle_4_deg 10.949 r_dihedral_angle_1_deg 5.244 r_scangle_it 2.549 r_scbond_it 1.472 r_angle_refined_deg 1.078 r_mcangle_it 0.986 r_mcbond_it 0.522 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.092 r_dihedral_angle_3_deg 14.261 r_dihedral_angle_4_deg 10.949 r_dihedral_angle_1_deg 5.244 r_scangle_it 2.549 r_scbond_it 1.472 r_angle_refined_deg 1.078 r_mcangle_it 0.986 r_mcbond_it 0.522 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2150 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 51
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling