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DNA polymerase X from Thermus thermophilus HB8 complexed with Ca-dGTP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.2M potassium chloride, 0.01M calcium chloride, 0.005M sodium cacodylate (pH 6.0), 10% PEG 4000 (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 47.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.189 α = 90 b = 53.286 β = 107.52 c = 84.877 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 93 CCD MARMOSAIC 225 mm CCD 2009-10-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0000, 0.978954, 0.979311 SPring-8 BL26B2
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 1.4 80.94 98.5 0.043 52.2 7.5 116175 114469
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 1.4 1.42 97.2 0.256 6.56 6.8 5566
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.4 50 108638 5714 98.43 0.16304 0.16169 0.18844 0.1919 RANDOM 21.931
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] -0.33 0.06 0.77 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.286 r_dihedral_angle_4_deg 15.869 r_dihedral_angle_3_deg 12.854 r_sphericity_free 6.046 r_dihedral_angle_1_deg 5.554 r_sphericity_bonded 4.549 r_scangle_it 4.22 r_scbond_it 2.721 r_mcangle_it 1.93 r_rigid_bond_restr 1.397
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.286 r_dihedral_angle_4_deg 15.869 r_dihedral_angle_3_deg 12.854 r_sphericity_free 6.046 r_dihedral_angle_1_deg 5.554 r_sphericity_bonded 4.549 r_scangle_it 4.22 r_scbond_it 2.721 r_mcangle_it 1.93 r_rigid_bond_restr 1.397 r_angle_refined_deg 1.377 r_mcbond_it 1.199 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4523 Nucleic Acid Atoms Solvent Atoms 622 Heterogen Atoms 39
Software Software Software Name Purpose HKL-2000 data collection SOLVE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling