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Crystal structure of human ALKBH7 in complex with N-oxalylglycine 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 pH 6 , EVAPORATION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.364 α = 90 b = 81.958 β = 119.94 c = 66.082 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 133 CCD MAR CCD 165 mm 2013-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 0.97908 BSRF 3W1A
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 1.99 50 96.7 42138 40730 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 2 2.03 80.5
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 1.99 33.37 3 40730 38211 2020 95.64 0.15925 0.15925 0.15895 0.1572 0.16516 0.1621 RANDOM 34.608
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] -15.5 10.02 26.03 -10.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.508 r_dihedral_angle_4_deg 17.248 r_dihedral_angle_3_deg 16.78 r_dihedral_angle_1_deg 6.876 r_long_range_B_refined 4.659 r_long_range_B_other 4.614 r_mcangle_it 3.003 r_mcangle_other 3.003 r_scangle_other 2.501 r_mcbond_other 2.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.508 r_dihedral_angle_4_deg 17.248 r_dihedral_angle_3_deg 16.78 r_dihedral_angle_1_deg 6.876 r_long_range_B_refined 4.659 r_long_range_B_other 4.614 r_mcangle_it 3.003 r_mcangle_other 3.003 r_scangle_other 2.501 r_mcbond_other 2.065 r_mcbond_it 2.064 r_scbond_it 1.711 r_scbond_other 1.704 r_angle_refined_deg 1.324 r_angle_other_deg 0.789 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4506 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 24
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling