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PRECATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH GAPPED DNA SUBSTARTE, INCOMING L-DCTP AND CA2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RPX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 50 MM IMIDAZOLE, 350 MM SODIUM
ACETATE, 17% PEG3350,
Crystal Properties Matthews coefficient Solvent content 2.22 44.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.91 α = 90 b = 80.16 β = 107.68 c = 55.64 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 193 CCD RAYONIX MX225HE 2013-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 26.96 99.8 0.112 8.9 5.4 39460
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 100 0.632 2.5 5.3
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 4RPX 1.8 26.96 37460 1978 99.8 0.192 0.191 0.1969 0.229 0.2313 RANDOM 20.28
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] 0.06 -0.04 0.1 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.888 r_dihedral_angle_4_deg 16.484 r_dihedral_angle_3_deg 13.889 r_dihedral_angle_1_deg 4.916 r_long_range_B_refined 3.946 r_long_range_B_other 3.78 r_scangle_other 2.13 r_mcangle_it 1.699 r_mcangle_other 1.698 r_scbond_it 1.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.888 r_dihedral_angle_4_deg 16.484 r_dihedral_angle_3_deg 13.889 r_dihedral_angle_1_deg 4.916 r_long_range_B_refined 3.946 r_long_range_B_other 3.78 r_scangle_other 2.13 r_mcangle_it 1.699 r_mcangle_other 1.698 r_scbond_it 1.293 r_scbond_other 1.293 r_angle_refined_deg 1.148 r_mcbond_it 0.99 r_mcbond_other 0.986 r_angle_other_deg 0.839 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2633 Nucleic Acid Atoms 632 Solvent Atoms 286 Heterogen Atoms 44
Software Software Software Name Purpose MOSFLM data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement