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Crystal structure of RecJCdc45 from Methanothermobacter thermoautotroficus in complex with ssDNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TVV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M bis-Tris pH 5.5, 17% w/v PEG 10000, 1M NH4CH3CO2
Crystal Properties Matthews coefficient Solvent content 2.56 51.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.08 α = 86.12 b = 69.501 β = 69.26 c = 72.21 γ = 69.53
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 S 6M 2018-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.9789 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.7 67.39 98.1 0.984 9.6 3.1 11350
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 0.673 1.9
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 6TVV 2.7 67.38 10315 1462 97.68 0.1997 0.1963 0.1987 0.2584 0.2562 RANDOM 62.605
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] 3.15 0.21 -1.35 -3.87 -0.69 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.206 r_dihedral_angle_3_deg 18.877 r_dihedral_angle_4_deg 18.723 r_dihedral_angle_1_deg 7.589 r_angle_refined_deg 1.674 r_angle_other_deg 1.187 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.206 r_dihedral_angle_3_deg 18.877 r_dihedral_angle_4_deg 18.723 r_dihedral_angle_1_deg 7.589 r_angle_refined_deg 1.674 r_angle_other_deg 1.187 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6496 Nucleic Acid Atoms 492 Solvent Atoms 39 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing