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DNA binding domain of J-DNA Binding Protein 1 (JBP1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XSE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 15-17% Peg 6000, 0.1M Sodium iodide or 15-17% Peg, 0.2M potassium nitrate
Crystal Properties Matthews coefficient Solvent content 3.05 59.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.286 α = 90 b = 68.286 β = 90 c = 185.842 γ = 120
Symmetry Space Group P 61 2 2
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 9M 2018-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.98 NSLS-II 17-ID-1
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 1.95 29.6 100 0.157 17.5 38.4 19605 32.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 5.033
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2XSE 1.95 29.59 18522 1017 99.93 0.20453 0.20204 0.2064 0.25194 0.2607 RANDOM 54.275
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] 0.77 0.39 0.77 -2.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.11 r_dihedral_angle_3_deg 13.895 r_dihedral_angle_4_deg 11.894 r_long_range_B_refined 7.393 r_long_range_B_other 7.345 r_dihedral_angle_1_deg 5.09 r_scangle_other 4.379 r_mcangle_it 3.227 r_mcangle_other 3.227 r_scbond_it 2.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.11 r_dihedral_angle_3_deg 13.895 r_dihedral_angle_4_deg 11.894 r_long_range_B_refined 7.393 r_long_range_B_other 7.345 r_dihedral_angle_1_deg 5.09 r_scangle_other 4.379 r_mcangle_it 3.227 r_mcangle_other 3.227 r_scbond_it 2.762 r_scbond_other 2.759 r_mcbond_it 2.13 r_mcbond_other 2.119 r_angle_refined_deg 1.621 r_angle_other_deg 1.142 r_chiral_restr 0.097 r_bond_refined_d 0.013 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 1400 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB-REDO refinement XDS data reduction MOLREP phasing