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DNA binding domain of J-DNA Binding Protein 3 (JBP3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other OneDep ID : D_1292141777
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 2.04 39.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.701 α = 90 b = 40.937 β = 123.816 c = 100.595 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 PILATUS 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) 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 1.7 83.576 99 0.05 11.1 2.9 41694 23.5
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 1.7 1.73 0.63 0.736 0.75 2.9
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 1.7 83.576 41665 2114 98.357 0.176 0.174 0.1836 0.2116 0.2158 34.999
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] -0.95 -0.421 0.315 0.632
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.252 r_dihedral_angle_3_deg 11.904 r_lrange_other 10.887 r_lrange_it 10.87 r_dihedral_angle_1_deg 8.689 r_scangle_it 8.155 r_scangle_other 8.151 r_scbond_it 5.492 r_scbond_other 5.491 r_mcangle_it 5.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.252 r_dihedral_angle_3_deg 11.904 r_lrange_other 10.887 r_lrange_it 10.87 r_dihedral_angle_1_deg 8.689 r_scangle_it 8.155 r_scangle_other 8.151 r_scbond_it 5.492 r_scbond_other 5.491 r_mcangle_it 5.47 r_mcangle_other 5.468 r_mcbond_it 3.715 r_mcbond_other 3.708 r_angle_refined_deg 1.164 r_angle_other_deg 0.449 r_nbd_refined 0.215 r_symmetry_nbd_refined 0.215 r_nbtor_refined 0.184 r_symmetry_nbd_other 0.17 r_nbd_other 0.166 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.141 r_ncsr_local_group_1 0.112 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.06 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3109 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing PDB-REDO refinement