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Grimontia hollisae thermostable direct hemolysin in complex with 1-nt long 3'-overhang dsDNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WX3 Thermostable direct hemolysin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 200 mM Ammonium sulfate, 100 mM Bis Tris/ Hydrochloric acid pH 5.5
Crystal Properties Matthews coefficient Solvent content 3.3 62.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.191 α = 90 b = 61.644 β = 104.67 c = 113.461 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 PIXEL DECTRIS EIGER2 X 9M 2023-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1.0 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.32 28.232 99.2 0.052 20.4 3.3 46053
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.32 2.4 0.341
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 2.32 28.23 41292 2146 94.01 0.21641 0.21461 0.2218 0.25081 0.2563 RANDOM 33.226
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.109 r_long_range_B_other 9.536 r_long_range_B_refined 9.53 r_dihedral_angle_2_deg 9.321 r_dihedral_angle_1_deg 7.855 r_scangle_other 7.618 r_mcangle_it 4.972 r_mcangle_other 4.972 r_scbond_it 4.678 r_scbond_other 4.673
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.109 r_long_range_B_other 9.536 r_long_range_B_refined 9.53 r_dihedral_angle_2_deg 9.321 r_dihedral_angle_1_deg 7.855 r_scangle_other 7.618 r_mcangle_it 4.972 r_mcangle_other 4.972 r_scbond_it 4.678 r_scbond_other 4.673 r_mcbond_it 3.171 r_mcbond_other 3.17 r_angle_refined_deg 1.457 r_angle_other_deg 0.529 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.003 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 4788 Nucleic Acid Atoms 446 Solvent Atoms 187 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling Coot model building HKL-2000 data reduction