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crystal structure of human ABH2 cross-linked to dsDNA with cofactors
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 298 16% PEG 4000, 0.1M sodium chloride, 0.05M magnesium chloride, 0.1M cacodylate, 0.001M MnCl2, 0.002M 2-ketoglutarate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.18 61.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.591 α = 90 b = 77.591 β = 90 c = 227.051 γ = 120
Symmetry Space Group P 65 2 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
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 2.5 33.2 99.8 0.086 20.6 8.6 14823 14823
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 2.5 2.54 100 0.498 3.5 8.4 690
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 MOLECULAR REPLACEMENT THROUGHOUT 2.5 20 13964 749 99.74 0.23305 0.23029 0.2159 0.28394 0.2618 RANDOM 36.953
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] -1.33 -0.67 -1.33 2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.203 r_dihedral_angle_4_deg 16.335 r_dihedral_angle_3_deg 13.548 r_dihedral_angle_1_deg 5.369 r_scangle_it 1.517 r_angle_refined_deg 1.192 r_scbond_it 0.916 r_mcangle_it 0.639 r_mcbond_it 0.351 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.203 r_dihedral_angle_4_deg 16.335 r_dihedral_angle_3_deg 13.548 r_dihedral_angle_1_deg 5.369 r_scangle_it 1.517 r_angle_refined_deg 1.192 r_scbond_it 0.916 r_mcangle_it 0.639 r_mcbond_it 0.351 r_nbtor_refined 0.3 r_nbd_refined 0.177 r_symmetry_vdw_refined 0.166 r_symmetry_hbond_refined 0.13 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 1631 Nucleic Acid Atoms 527 Solvent Atoms 91 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASES phasing