☰ Navigation Tabs
DNA binding domain of J-DNA Binding Protein 3 (JBP3)
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 277 0.2 M potassium sodium tartrate tetrahydrate, 20% w/v polyethylane glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.27 45.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.828 α = 90 b = 59.678 β = 90 c = 67.288 γ = 90
Symmetry Space Group P 2 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 PILATUS3 6M 2017-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.966 ESRF ID30B
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 1.615 44.648 100 0.078 0.999 13.4 6.3 24706 21.9
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 1.62 1.64 1.97 0.142 0.79
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.615 44.648 24670 1211 99.312 0.192 0.1903 0.1996 0.2219 0.2269 31.777
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] -1.531 0.638 0.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.566 r_dihedral_angle_1_deg 13.922 r_dihedral_angle_3_deg 11.891 r_lrange_it 7.143 r_lrange_other 7.105 r_scangle_it 5.09 r_scangle_other 5.088 r_mcangle_it 3.535 r_mcangle_other 3.535 r_scbond_it 3.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.566 r_dihedral_angle_1_deg 13.922 r_dihedral_angle_3_deg 11.891 r_lrange_it 7.143 r_lrange_other 7.105 r_scangle_it 5.09 r_scangle_other 5.088 r_mcangle_it 3.535 r_mcangle_other 3.535 r_scbond_it 3.225 r_scbond_other 3.223 r_mcbond_it 2.208 r_mcbond_other 2.187 r_angle_refined_deg 1.24 r_angle_other_deg 0.499 r_symmetry_xyhbond_nbd_refined 0.215 r_nbd_refined 0.202 r_nbtor_refined 0.177 r_symmetry_nbd_other 0.155 r_xyhbond_nbd_refined 0.144 r_symmetry_nbd_refined 0.121 r_nbd_other 0.106 r_symmetry_nbtor_other 0.065 r_chiral_restr 0.059 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1375 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling MOLREP phasing PDB-REDO refinement