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Structure of human ALKBH5 crystallized in the presence of citrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H8R PDB ENTRY 3H8R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 291 20% PEG3350, 0.2 M diammonium citrate, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.19 43.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.471 α = 90 b = 57.172 β = 102.23 c = 78.644 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 2013-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 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 1.9 38.43 100 0.129 13.7 7.2 34700
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 1.9 1.94 100 0.983 2.2 7.1 2237
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3H8R 1.9 30 34660 1810 99.83 0.1767 0.1738 0.1871 0.2303 0.2358 THIN SHELLS (SFTOOLS) 23.5301
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] 2.08 -1.07 -0.12 -1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.37 r_dihedral_angle_4_deg 20.388 r_dihedral_angle_3_deg 13.116 r_dihedral_angle_1_deg 5.951 r_mcangle_it 3.098 r_mcbond_other 2.112 r_mcbond_it 2.111 r_angle_refined_deg 1.457 r_angle_other_deg 0.806 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.37 r_dihedral_angle_4_deg 20.388 r_dihedral_angle_3_deg 13.116 r_dihedral_angle_1_deg 5.951 r_mcangle_it 3.098 r_mcbond_other 2.112 r_mcbond_it 2.111 r_angle_refined_deg 1.457 r_angle_other_deg 0.806 r_chiral_restr 0.092 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3288 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 76
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data scaling BALBES phasing