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Human AlkB homolog ALKBH6 in complex with Tris and Ni
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3THP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 PEG 8000, Tris
Crystal Properties Matthews coefficient Solvent content 2.64 53.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.374 α = 90 b = 64.212 β = 90 c = 88.96 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 2M 2019-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9793 SSRF BL17U
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 1.79 50 99.8 0.994 31.5 7.1 25643
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 1.79 1.82 0.612
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3THP 1.792 19.724 25396 1261 99.06 0.198 0.1969 0.2053 0.2144 0.2198 22.654
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] -0.003 -0.024 0.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.463 r_dihedral_angle_4_deg 14.212 r_dihedral_angle_3_deg 12.416 r_dihedral_angle_1_deg 7.203 r_lrange_it 4.905 r_lrange_other 4.853 r_scangle_it 3.905 r_scangle_other 3.903 r_mcangle_other 2.806 r_mcangle_it 2.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.463 r_dihedral_angle_4_deg 14.212 r_dihedral_angle_3_deg 12.416 r_dihedral_angle_1_deg 7.203 r_lrange_it 4.905 r_lrange_other 4.853 r_scangle_it 3.905 r_scangle_other 3.903 r_mcangle_other 2.806 r_mcangle_it 2.796 r_scbond_it 2.482 r_scbond_other 2.48 r_mcbond_it 1.923 r_mcbond_other 1.865 r_angle_refined_deg 1.467 r_angle_other_deg 1.305 r_nbd_refined 0.205 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.162 r_nbd_other 0.147 r_symmetry_xyhbond_nbd_refined 0.134 r_xyhbond_nbd_refined 0.132 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_symmetry_nbd_refined 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1562 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling BALBES phasing