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Structure of the NHEJ polymerase from Methanocella paludicola
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IRU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 285 200 mM ammonium sulfate, 20% (w/v) PEG 335
Crystal Properties Matthews coefficient Solvent content 2.3 46.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.42 α = 90 b = 60.55 β = 101.02 c = 59.41 γ = 90
Symmetry Space Group P 1 21 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 CCD RIGAKU SATURN 944+ VariMax-HF mirrors 2013-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim 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 1.949 58.315 97.4 0.071 0.084 0.044 13.8 3.5 22140 22140
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.05 84 0.2 0.2 0.14 3.8 2.6 2768
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 2IRU 1.949 58.31 20996 1131 97.35 0.1502 0.1478 0.1497 0.1954 0.198 RANDOM 15.014
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] -0.13 0.13 0.02 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.897 r_dihedral_angle_4_deg 17.897 r_dihedral_angle_3_deg 14.442 r_dihedral_angle_1_deg 6.806 r_scbond_it 2.359 r_angle_refined_deg 1.82 r_mcangle_it 1.701 r_mcbond_it 1.094 r_chiral_restr 0.135 r_bond_refined_d 0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.897 r_dihedral_angle_4_deg 17.897 r_dihedral_angle_3_deg 14.442 r_dihedral_angle_1_deg 6.806 r_scbond_it 2.359 r_angle_refined_deg 1.82 r_mcangle_it 1.701 r_mcbond_it 1.094 r_chiral_restr 0.135 r_bond_refined_d 0.019 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2404 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction PHASER phasing PDB_EXTRACT data extraction CrystalClear data collection SCALA data scaling Coot model building