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Crystal structure of periplasmic solute binding protein ECA2210 from Pectobacterium atrosepticum SCRI1043, Target EFI-510858
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294 PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT); RESERVOIR: 0.085 M TRIS-HCL, PH 8.5, 0.17 M SODIUM ACETATE, 25% PEG3350, 15% (V/V) GLYCEROL; CRYOPROTECTION: RESERVOIR SOLUTION, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.28 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.751 α = 90 b = 93.669 β = 90.19 c = 99.148 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 CCD RAYONIX MX225HE MIRRORS 2014-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID APS 31-ID
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 1.4 50 99.9 0.104 22.2 7.6 160376 -3
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 1.4 1.42 100 0.69 2.9 6.5
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 SAD THROUGHOUT 1.4 50 155400 4743 99.85 0.13739 0.13612 0.1454 0.17647 0.1816 RANDOM 23.053
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] 0.18 0.06 -0.66 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.634 r_sphericity_free 29.248 r_dihedral_angle_4_deg 18.828 r_sphericity_bonded 15.038 r_dihedral_angle_3_deg 14.314 r_scbond_it 7.194 r_scbond_other 7.193 r_scangle_other 6.876 r_long_range_B_refined 6.03 r_long_range_B_other 6.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.634 r_sphericity_free 29.248 r_dihedral_angle_4_deg 18.828 r_sphericity_bonded 15.038 r_dihedral_angle_3_deg 14.314 r_scbond_it 7.194 r_scbond_other 7.193 r_scangle_other 6.876 r_long_range_B_refined 6.03 r_long_range_B_other 6.03 r_dihedral_angle_1_deg 5.496 r_mcangle_it 3.906 r_mcangle_other 3.905 r_mcbond_it 3.875 r_mcbond_other 3.871 r_rigid_bond_restr 3.134 r_angle_refined_deg 1.461 r_angle_other_deg 0.988 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6374 Nucleic Acid Atoms Solvent Atoms 1014 Heterogen Atoms 44
Software Software Software Name Purpose SHELX model building ARP/wARP model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling SHELX phasing