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Crystal structure of HsmR with DNA bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8ZA5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 0.1 M KCl, 35% PEP (5/4 PO/OH) and 50 mM HEPES (pH 7.5)
Crystal Properties Matthews coefficient Solvent content 2.68 54.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 262.113 α = 90 b = 55.705 β = 101.35 c = 117.525 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 CCD ADSC QUANTUM 270 2023-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97179 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.9 50 99.6 0.133 0.991 18.9 3.5 37178
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.95 1.093 0.888
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 2.91 50 35124 1857 99.14 0.21573 0.21247 0.2346 0.27599 0.2903 RANDOM
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] 1.3 7.02 2.34 -5.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.851 r_dihedral_angle_3_deg 20.428 r_dihedral_angle_4_deg 15.806 r_long_range_B_refined 13.846 r_long_range_B_other 13.845 r_scangle_other 10.131 r_mcangle_it 9.604 r_mcangle_other 9.603 r_dihedral_angle_1_deg 7.583 r_scbond_it 6.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.851 r_dihedral_angle_3_deg 20.428 r_dihedral_angle_4_deg 15.806 r_long_range_B_refined 13.846 r_long_range_B_other 13.845 r_scangle_other 10.131 r_mcangle_it 9.604 r_mcangle_other 9.603 r_dihedral_angle_1_deg 7.583 r_scbond_it 6.309 r_scbond_other 6.309 r_mcbond_it 6.042 r_mcbond_other 6.032 r_angle_refined_deg 1.453 r_angle_other_deg 1.239 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6810 Nucleic Acid Atoms 2688 Solvent Atoms 24 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing