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Crystal structure of the carboxyl-terminal domain of yeast DNA polymerase alpha in complex with its B subunit
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 0.1M MES, 1.26M Ammonium Sulfate, 3mM TCEP, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.42 64.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.411 α = 90 b = 142.633 β = 102.33 c = 175.255 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 ADSC Q315R silicon monochromator 2007-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 31.9 99.8 0.102 0.102 5.2 7.3 141597 141597 58.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 99.7 0.652 0.652 1.2 7.4 20778
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 SAD THROUGHOUT 2.5 31.9 134185 7082 99.8 0.192 0.191 0.2149 0.218 0.2359 RANDOM 43.61
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] 0.51 -0.45 -0.8 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.132 r_dihedral_angle_4_deg 20.359 r_dihedral_angle_3_deg 15.726 r_dihedral_angle_1_deg 6.323 r_scangle_it 2.746 r_scbond_it 2.056 r_angle_refined_deg 1.545 r_mcangle_it 1.154 r_mcbond_it 0.997 r_angle_other_deg 0.976
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.132 r_dihedral_angle_4_deg 20.359 r_dihedral_angle_3_deg 15.726 r_dihedral_angle_1_deg 6.323 r_scangle_it 2.746 r_scbond_it 2.056 r_angle_refined_deg 1.545 r_mcangle_it 1.154 r_mcbond_it 0.997 r_angle_other_deg 0.976 r_nbd_refined 0.21 r_symmetry_vdw_other 0.209 r_nbd_other 0.199 r_symmetry_hbond_refined 0.198 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.159 r_xyhbond_nbd_other 0.152 r_mcbond_other 0.136 r_symmetry_vdw_refined 0.127 r_chiral_restr 0.09 r_nbtor_other 0.09 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.002 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19648 Nucleic Acid Atoms Solvent Atoms 571 Heterogen Atoms 333
Software Software Software Name Purpose ADSC data collection PHENIX model building REFMAC refinement MOSFLM data reduction SCALA data scaling PHENIX phasing