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DNA polymerase D large subunit DP2(1-300) from Pyrococcus horikoshii
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 22.5% PEG 10000, 0.1M HEPES-NaOH, 40mM guanidine-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.87 34.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.042 α = 90 b = 54.042 β = 90 c = 173.335 γ = 90
Symmetry Space Group P 43 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 ADSC QUANTUM 4r mirror 2002-11-23 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.9788, 0.9793, 0.9900 Photon Factory BL-6A
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 2.2 50 99 0.058 77.9 27.3 13924 30.2
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) 2.2 2.28 92.4 0.233 14.4
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 MAD THROUGHOUT 2.2 43.33 12379 1362 99.39 0.21246 0.20626 0.2069 0.27168 0.2665 RANDOM 31.1
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] 0.23 0.23 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.133 r_dihedral_angle_4_deg 18.472 r_dihedral_angle_3_deg 17.856 r_dihedral_angle_1_deg 5.759 r_scangle_it 5.012 r_scbond_it 3.127 r_mcangle_it 1.805 r_angle_refined_deg 1.774 r_mcbond_it 0.989 r_chiral_restr 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.133 r_dihedral_angle_4_deg 18.472 r_dihedral_angle_3_deg 17.856 r_dihedral_angle_1_deg 5.759 r_scangle_it 5.012 r_scbond_it 3.127 r_mcangle_it 1.805 r_angle_refined_deg 1.774 r_mcbond_it 0.989 r_chiral_restr 0.117 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 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 1909 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection SHARP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling