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Crystal structure of SbnH in complex with citryl-diaminoethane
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J66
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 290 0.2 M Na Citrate, 50 mM Bis-Tris pH 6.0, 23% PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.94 58.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.299 α = 90 b = 80.325 β = 102.07 c = 111.524 γ = 90
Symmetry Space Group C 1 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 PILATUS3 S 6M 2018-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9791 SSRF BL19U1
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 2.3 46.74 97.3 0.047 15.1 3.3 65898
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 2.3 2.35 0.367
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 2J66 2.3 46.74 62570 3242 96.97 0.222 0.2208 0.2271 0.2455 0.2506 RANDOM 41.074
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] 0.92 -0.51 5.29 -5.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.9 r_dihedral_angle_3_deg 12.532 r_dihedral_angle_4_deg 12.131 r_dihedral_angle_1_deg 5.834 r_long_range_B_refined 2.471 r_long_range_B_other 2.471 r_mcangle_it 1.333 r_mcangle_other 1.333 r_scangle_other 1.143 r_angle_refined_deg 1.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.9 r_dihedral_angle_3_deg 12.532 r_dihedral_angle_4_deg 12.131 r_dihedral_angle_1_deg 5.834 r_long_range_B_refined 2.471 r_long_range_B_other 2.471 r_mcangle_it 1.333 r_mcangle_other 1.333 r_scangle_other 1.143 r_angle_refined_deg 1.087 r_angle_other_deg 0.879 r_mcbond_other 0.758 r_mcbond_it 0.757 r_scbond_it 0.634 r_scbond_other 0.633 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 9187 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing