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X-ray structure of Enterobacter cloacae allose-binding protein in complex with D-psicose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RPJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 293 20 mM D-psicose, 100 mM sodium citrate tribasic dihydrate, 22% (w/v) polyethylene glycol 1,000
Crystal Properties Matthews coefficient Solvent content 2.42 49.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.11 α = 90 b = 113.14 β = 90 c = 38.95 γ = 90
Symmetry Space Group P 21 21 2
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 6M 2022-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 1.71 43.29 98.1 0.999 27.6 6.4 32299
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 1.71 1.75 0.911
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 1RPJ 1.71 43.29 30708 1591 98.12 0.17125 0.16747 0.1767 0.24208 0.2473 RANDOM 31.992
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] -0.29 0.14 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.15 r_dihedral_angle_4_deg 24.993 r_dihedral_angle_3_deg 16.295 r_scbond_it 8.521 r_scbond_other 8.517 r_scangle_other 8.228 r_rigid_bond_restr 7.454 r_dihedral_angle_1_deg 7.394 r_mcangle_other 5.224 r_mcangle_it 5.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.15 r_dihedral_angle_4_deg 24.993 r_dihedral_angle_3_deg 16.295 r_scbond_it 8.521 r_scbond_other 8.517 r_scangle_other 8.228 r_rigid_bond_restr 7.454 r_dihedral_angle_1_deg 7.394 r_mcangle_other 5.224 r_mcangle_it 5.22 r_mcbond_it 4.768 r_angle_other_deg 1.293 r_angle_refined_deg 1.268 r_chiral_restr 0.06 r_gen_planes_refined 0.015 r_bond_refined_d 0.007 r_gen_planes_other 0.004 r_bond_other_d 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 2141 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing