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Crystal structure of RecJ-Cdc45 from Methanothermobacter Thermoautotrophicus
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 Tris/HCl pH 8.5, 27% w/v PEG 4000, 0.2M MgCl2*6H20, 1mM MnCl2
Crystal Properties Matthews coefficient Solvent content 1.95 36.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.471 α = 81.38 b = 55.01 β = 86.36 c = 89.99 γ = 89.95
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 2016-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 0.9724 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 2.7 88.79 92.8 0.97 3.5 1.7 19511
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 2.85 90.4 0.83 1.6
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 88.79 18487 1012 92.71 0.2326 0.2305 0.2328 0.2705 0.2714 RANDOM 30.098
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] -1.69 -0.75 -0.23 0.67 1.35 1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.661 r_dihedral_angle_3_deg 17.456 r_dihedral_angle_4_deg 16.159 r_dihedral_angle_1_deg 6.49 r_angle_refined_deg 1.483 r_angle_other_deg 1.113 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.661 r_dihedral_angle_3_deg 17.456 r_dihedral_angle_4_deg 16.159 r_dihedral_angle_1_deg 6.49 r_angle_refined_deg 1.483 r_angle_other_deg 1.113 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6293 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 4
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing