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Crystal structure of human ALKBH7 in complex with alpha-ketoglutarate and Mn(II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QKB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6 277 PEG pH6, EVAPORATION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.31 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.426 α = 90 b = 82.048 β = 120.03 c = 66.414 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 130 CCD ADSC QUANTUM 315 2012-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97930 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.35 50 91.9 135021 124116 3 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.37 61
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 4QKB 1.35 33.4 3 124116 117785 6254 91.77 0.14648 0.14648 0.14561 0.1526 0.16275 0.1556 RANDOM 17.989
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] -5.62 2.82 12.12 -6.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.04 r_sphericity_free 21.627 r_dihedral_angle_4_deg 18.469 r_dihedral_angle_3_deg 12.09 r_dihedral_angle_1_deg 6.504 r_sphericity_bonded 6.371 r_long_range_B_refined 3.252 r_long_range_B_other 2.483 r_rigid_bond_restr 2.395 r_scangle_other 1.999
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.04 r_sphericity_free 21.627 r_dihedral_angle_4_deg 18.469 r_dihedral_angle_3_deg 12.09 r_dihedral_angle_1_deg 6.504 r_sphericity_bonded 6.371 r_long_range_B_refined 3.252 r_long_range_B_other 2.483 r_rigid_bond_restr 2.395 r_scangle_other 1.999 r_mcangle_it 1.828 r_mcangle_other 1.828 r_scbond_other 1.771 r_scbond_it 1.769 r_mcbond_it 1.63 r_mcbond_other 1.623 r_angle_refined_deg 1.348 r_angle_other_deg 0.759 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 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 4499 Nucleic Acid Atoms Solvent Atoms 731 Heterogen Atoms 37
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling