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Crystal structure of RecJCdc45 from Methanothermobacter thermoautotroficus in complex with dCTP
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 propane pH 6.5, 14% w/v PEG 3350, 0.2M sodium nitrate, 1mM MnCl2
Crystal Properties Matthews coefficient Solvent content 2.19 43.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.75 α = 79.86 b = 53.88 β = 82.77 c = 86.72 γ = 63.98
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 2017-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0 ELETTRA 5.2R
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 2.2 48.23 97.6 0.942 3.4 2 42571
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 2.2 2.27 0.831 2
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 2.2 42.21 42570 2785 94.67 0.2558 0.2535 0.2631 0.2991 0.2581 RANDOM 30.87
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] 0.01 -0.01 0.16 0.09 -0.01 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.05 r_dihedral_angle_3_deg 17.494 r_dihedral_angle_4_deg 17.047 r_dihedral_angle_1_deg 6.531 r_angle_refined_deg 1.805 r_angle_other_deg 1.124 r_chiral_restr 0.126 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.05 r_dihedral_angle_3_deg 17.494 r_dihedral_angle_4_deg 17.047 r_dihedral_angle_1_deg 6.531 r_angle_refined_deg 1.805 r_angle_other_deg 1.124 r_chiral_restr 0.126 r_bond_refined_d 0.016 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 6491 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling MOLREP phasing