☰ Navigation Tabs
Archaeal histone protein HTkC from Thermococcus kodakarensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.01 M trisodium citrate and 33% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.5 50.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.655 α = 90 b = 64.294 β = 90 c = 79.846 γ = 90
Symmetry Space Group P 21 21 21
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 2023-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 SLS X10SA
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 1.84 44 99.6 0.107 0.998 12.63 7.16 24121
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 1.84 1.95 99 1.48 0.655 1.36 7.15
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 1.84 44 22916 1205 99.56 0.20508 0.20348 0.2108 0.23649 0.2464 RANDOM 29.242
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] 1.4 -0.78 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.457 r_dihedral_angle_4_deg 16.006 r_dihedral_angle_3_deg 12.267 r_dihedral_angle_1_deg 4.29 r_long_range_B_refined 4.189 r_long_range_B_other 3.926 r_scangle_other 1.831 r_mcangle_it 1.265 r_angle_other_deg 1.264 r_mcangle_other 1.264
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.457 r_dihedral_angle_4_deg 16.006 r_dihedral_angle_3_deg 12.267 r_dihedral_angle_1_deg 4.29 r_long_range_B_refined 4.189 r_long_range_B_other 3.926 r_scangle_other 1.831 r_mcangle_it 1.265 r_angle_other_deg 1.264 r_mcangle_other 1.264 r_angle_refined_deg 1.263 r_scbond_it 1.091 r_scbond_other 1.09 r_mcbond_it 0.79 r_mcbond_other 0.788 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 1789 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing