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Human APE1 in complex with DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QHD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.15 M ammonium sulfate, 0.1 M Na HEPES pH 7, 20% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.28 46.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.122 α = 90 b = 71.707 β = 110.571 c = 75.274 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS EIGER2 XE 16M 2024-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.90931 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.7 35.85 99.3 0.999 12.7 6.8 38179
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 0.876 1.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.7 35.838 38177 1844 99.249 0.194 0.1925 0.1979 0.2279 0.233 31.325
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] -0.452 -1.944 2.152 -0.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.811 r_dihedral_angle_3_deg 13.621 r_dihedral_angle_2_deg 8.301 r_dihedral_angle_1_deg 7.134 r_lrange_it 6.654 r_lrange_other 6.626 r_scangle_it 4.198 r_scangle_other 4.197 r_scbond_it 2.687 r_scbond_other 2.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.811 r_dihedral_angle_3_deg 13.621 r_dihedral_angle_2_deg 8.301 r_dihedral_angle_1_deg 7.134 r_lrange_it 6.654 r_lrange_other 6.626 r_scangle_it 4.198 r_scangle_other 4.197 r_scbond_it 2.687 r_scbond_other 2.686 r_mcangle_it 2.088 r_mcangle_other 2.088 r_angle_refined_deg 1.706 r_mcbond_it 1.304 r_mcbond_other 1.302 r_dihedral_angle_other_2_deg 0.978 r_angle_other_deg 0.535 r_symmetry_nbd_refined 0.244 r_nbd_refined 0.24 r_symmetry_xyhbond_nbd_refined 0.221 r_nbd_other 0.218 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.193 r_xyhbond_nbd_refined 0.145 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.079 r_gen_planes_refined 0.009 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2123 Nucleic Acid Atoms 485 Solvent Atoms 194 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing