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Crystal structure of domain-of-unknown-function DUF4867 from Bacillus megaterium (unmodelled additional ligand density at active site)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9GYY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Direct soaking of sulfofructose ligand into a crystal of SqvD, which was obtained from protein solution at 60 mg mL-1 in 50 mM Tris buffer, 300 mM NaCl buffer pH 7.5 used to set up a drop containing 0.15 uL protein: 0.15 uL mother liquor, the latter comprising 0.1 M HEPES sodium 7.5 30 % v/v polyethylene glycol 400.
Crystal Properties Matthews coefficient Solvent content 2.41 48.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.509 α = 90 b = 82.509 β = 90 c = 136.194 γ = 120
Symmetry Space Group P 32 2 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 EIGER2 X 16M 2021-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9763 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.1 49.3 100 0.101 0.104 0.025 0.999 17.2 16.7 32018
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 100 1.323 1.36 0.313 0.905 18.6
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 2.1 45.44 30237 1588 99.51 0.21014 0.2078 0.2153 0.25529 0.2576 RANDOM 48.115
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] 0.97 0.48 0.97 -3.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.442 r_long_range_B_other 10.225 r_long_range_B_refined 10.219 r_scangle_other 9.647 r_dihedral_angle_2_deg 9.058 r_dihedral_angle_1_deg 7.807 r_scbond_it 7.789 r_scbond_other 7.787 r_mcangle_it 7.032 r_mcangle_other 7.032
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.442 r_long_range_B_other 10.225 r_long_range_B_refined 10.219 r_scangle_other 9.647 r_dihedral_angle_2_deg 9.058 r_dihedral_angle_1_deg 7.807 r_scbond_it 7.789 r_scbond_other 7.787 r_mcangle_it 7.032 r_mcangle_other 7.032 r_mcbond_it 6.416 r_mcbond_other 6.416 r_angle_refined_deg 2.324 r_angle_other_deg 0.803 r_chiral_restr 0.12 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3482 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction MOLREP phasing