☰ Navigation Tabs
Crystal structure of domain-of-unknown-function DUF4867 from Bacillus megaterium
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 A crystal of ligand-free B. megaterium SqvD was grown using a 60 mg mL-1 protein solution in 50 mM TRIS buffer pH 7.5 containing 300 mM NaCl in a drop with 0.15 uL protein: 0.15 uL mother liquor, the latter comprising 2.0 M sodium chloride and 10 % w/v PEG (polyethylene glycol) 6,000.
Crystal Properties Matthews coefficient Solvent content 2.45 49.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.835 α = 90 b = 83.835 β = 90 c = 133.931 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 EIGER X 16M 2021-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.5 66.97 100 0.055 0.057 0.013 0.999 28.1 20 87735
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 1.5 1.53 100 1.103 1.131 0.247 0.881 20.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.5 63.91 83301 4373 99.99 0.17676 0.17565 0.19827 0.1975 RANDOM 24.346
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] -0.11 -0.05 -0.11 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.578 r_dihedral_angle_2_deg 7.544 r_dihedral_angle_1_deg 6.361 r_long_range_B_refined 5.31 r_scbond_it 3.326 r_mcangle_it 2.974 r_mcbond_it 2.174 r_angle_refined_deg 2.163 r_chiral_restr 0.139 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.578 r_dihedral_angle_2_deg 7.544 r_dihedral_angle_1_deg 6.361 r_long_range_B_refined 5.31 r_scbond_it 3.326 r_mcangle_it 2.974 r_mcbond_it 2.174 r_angle_refined_deg 2.163 r_chiral_restr 0.139 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3509 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction SHELXCD phasing