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Crystal structure of ESCHERICHIA coli DNA Polymerase II
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.3 295 Citrate , PEG3K, DTT, EDTA, Glycerol, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K 2 VAPOR DIFFUSION, HANGING DROP 5.5 295 Citrate , PEG3K, DTT, EDTA, Glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K 3 VAPOR DIFFUSION, HANGING DROP 5.8 295 Citrate , PEG3K, DTT, MgCl2, Glycerol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.383 α = 90 b = 116.596 β = 90 c = 82.43 γ = 90
Symmetry Space Group P 21 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 MARRESEARCH M SINGLE WAVELENGTH 2 1 x-ray 100 CCD CUSTOM-MADE M SINGLE WAVELENGTH 3 1 x-ray M 1,2,3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 1.0 APS 5ID-B 2 SYNCHROTRON APS BEAMLINE 5ID-B 1.0 APS 5ID-B 3 SYNCHROTRON APS BEAMLINE 19-ID 1.77 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1,2,3 2 29.7 60657
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MIRAS THROUGHOUT 2 20 57543 3064 99.76 0.19872 0.19672 0.2 0.23612 0.2397 RANDOM 26.269
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] -1.59 -0.64 2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.633 r_dihedral_angle_3_deg 18.472 r_scangle_it 8.99 r_scbond_it 6.473 r_dihedral_angle_1_deg 4.816 r_mcangle_it 4.285 r_mcbond_it 3.171 r_angle_refined_deg 1.636 r_symmetry_hbond_refined 0.283 r_nbd_refined 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.633 r_dihedral_angle_3_deg 18.472 r_scangle_it 8.99 r_scbond_it 6.473 r_dihedral_angle_1_deg 4.816 r_mcangle_it 4.285 r_mcbond_it 3.171 r_angle_refined_deg 1.636 r_symmetry_hbond_refined 0.283 r_nbd_refined 0.24 r_symmetry_vdw_refined 0.239 r_xyhbond_nbd_refined 0.204 r_chiral_restr 0.151 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5709 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MLPHARE phasing