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Ternary complex of DNA polymerase delta
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 12% PEG 4000, NaAc pH 5.5, 200mM CaAc., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.5 50.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.077 α = 90 b = 85.948 β = 111.1 c = 86.872 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 QUANTUM 315 2007-10-13 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 210 2007-08-29 M SINGLE WAVELENGTH 3 1 x-ray 100 CCD ADSC QUANTUM 315 2007-10-13 M MAD 4 1 x-ray 100 CCD ADSC QUANTUM 315 2007-11-08 M SINGLE WAVELENGTH 1,2,3,4 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A 2 SYNCHROTRON NSLS BEAMLINE X12B NSLS X12B 3 SYNCHROTRON APS BEAMLINE 17-ID APS 17-ID 4
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 1,2,3,4 2 41.52 98.3 73557 69856 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2,3,4 2 2.07 97.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 MIR THROUGHOUT 2 41.52 73557 69856 3692 98.25 0.19497 0.19281 0.1802 0.23589 0.2215 RANDOM 28.037
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] -0.29 0.5 0.56 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.958 r_dihedral_angle_4_deg 17.191 r_dihedral_angle_3_deg 14.138 r_dihedral_angle_1_deg 5.646 r_scangle_it 2.663 r_scbond_it 1.708 r_angle_refined_deg 1.227 r_mcangle_it 1.033 r_mcbond_it 0.554 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.958 r_dihedral_angle_4_deg 17.191 r_dihedral_angle_3_deg 14.138 r_dihedral_angle_1_deg 5.646 r_scangle_it 2.663 r_scbond_it 1.708 r_angle_refined_deg 1.227 r_mcangle_it 1.033 r_mcbond_it 0.554 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 6986 Nucleic Acid Atoms 569 Solvent Atoms 558 Heterogen Atoms 41
Software Software Software Name Purpose ADSC data collection SHARP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling