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Crystal structure of human ALKBH5 crystallized in the presence of Mn^{2+} and 2-oxoglutarate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4O61 related to pdb entry 4O61
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 0.005 M of each manganous sulfate and 2-oxyglutarate were added to the protein stock solution. Reservoir: 20% PEG-3350, 0.2 M diammonium phosphate, vapor diffusion, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.2 42.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.93 α = 90 b = 57.234 β = 101.07 c = 78.407 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE RIGAKU RAXIS 2013-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.5418
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 2.28 38.47 99.9 0.127 13.3 7.3 18808
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 2.28 2.36 100 0.011 2.1 7.1 1848
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION direct placement THROUGHOUT related to pdb entry 4O61 2.28 30 18790 934 99.76 0.2405 0.2382 0.2435 0.2841 0.2886 THIN SHELLS (SFTOOLS) 45.2232
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] -2.05 0.85 1.87 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.915 r_dihedral_angle_4_deg 18.784 r_dihedral_angle_3_deg 14.775 r_dihedral_angle_1_deg 6.479 r_mcangle_it 1.559 r_angle_refined_deg 1.401 r_mcbond_it 0.935 r_mcbond_other 0.935 r_angle_other_deg 0.878 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.915 r_dihedral_angle_4_deg 18.784 r_dihedral_angle_3_deg 14.775 r_dihedral_angle_1_deg 6.479 r_mcangle_it 1.559 r_angle_refined_deg 1.401 r_mcbond_it 0.935 r_mcbond_other 0.935 r_angle_other_deg 0.878 r_chiral_restr 0.077 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3248 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 45
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction