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Human AlkB homolog ALKBH6 in complex with alpha-katoglutarate and Mn
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 2.47 50.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.118 α = 90 b = 64.407 β = 90 c = 88.416 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 2019-11-10 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 1.75 50 98.67 0.977 15 4.5 27487
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 1.75 1.78 0.827
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 1.75 26.417 26981 1372 98.929 0.191 0.1901 0.2015 0.2068 0.212 20.296
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 0.01 -0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.252 r_dihedral_angle_4_deg 12.99 r_dihedral_angle_3_deg 12.27 r_dihedral_angle_1_deg 7.304 r_lrange_it 4.738 r_lrange_other 4.716 r_scangle_it 3.957 r_scangle_other 3.956 r_mcangle_other 2.6 r_mcangle_it 2.589
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.252 r_dihedral_angle_4_deg 12.99 r_dihedral_angle_3_deg 12.27 r_dihedral_angle_1_deg 7.304 r_lrange_it 4.738 r_lrange_other 4.716 r_scangle_it 3.957 r_scangle_other 3.956 r_mcangle_other 2.6 r_mcangle_it 2.589 r_scbond_it 2.552 r_scbond_other 2.552 r_mcbond_it 1.731 r_mcbond_other 1.7 r_angle_refined_deg 1.495 r_angle_other_deg 1.329 r_nbd_refined 0.209 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.163 r_symmetry_nbd_refined 0.162 r_nbd_other 0.129 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.077 r_symmetry_xyhbond_nbd_refined 0.055 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1707 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling BALBES phasing