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Crystal structure of DNA polymerase III, beta subunit (TM0262) from Thermotoga maritima at 2.00 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JQJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 4 293 6.25% PEG-6000, 0.1M Citrate pH 4.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.73 54.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.702 α = 90 b = 91.702 β = 90 c = 111.463 γ = 90
Symmetry Space Group P 42 21 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 CCD ADSC 2003-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 50 99.78 0.058 39.82 10.66 32639 46.77
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 99.65 0.809 2.25 8.58 3172
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 1JQJ 2 47.63 30962 1656 99.62 0.19814 0.19632 0.2044 0.23207 0.237 RANDOM 46.909
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] 0.11 0.11 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.794 r_dihedral_angle_4_deg 17.97 r_dihedral_angle_3_deg 14.727 r_dihedral_angle_1_deg 6.838 r_scangle_it 4.348 r_scbond_it 2.739 r_angle_refined_deg 1.668 r_mcangle_it 1.649 r_mcbond_it 1.174 r_angle_other_deg 0.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.794 r_dihedral_angle_4_deg 17.97 r_dihedral_angle_3_deg 14.727 r_dihedral_angle_1_deg 6.838 r_scangle_it 4.348 r_scbond_it 2.739 r_angle_refined_deg 1.668 r_mcangle_it 1.649 r_mcbond_it 1.174 r_angle_other_deg 0.835 r_mcbond_other 0.267 r_symmetry_vdw_refined 0.25 r_nbd_refined 0.206 r_symmetry_vdw_other 0.196 r_xyhbond_nbd_refined 0.184 r_nbd_other 0.177 r_nbtor_refined 0.173 r_symmetry_hbond_refined 0.124 r_chiral_restr 0.106 r_nbtor_other 0.087 r_bond_refined_d 0.018 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 2853 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement