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Crystal structure of human ALKBH5 in complex with Mn2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NRM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 289 20% PEG 4K, 100mM CH3CO2NH4, 100mM Na-citrate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.25 45.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.093 α = 90 b = 57.093 β = 90 c = 145.729 γ = 90
Symmetry Space Group P 43 21 2
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 2012-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 1.0 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 1.78 53.16 99.3 24002 23830 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 1.78 1.83 97
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4NRM 1.78 50 24002 23830 1179 99.2 0.2154 0.2154 0.21415 0.2114 0.23762 0.2318 RANDOM 32.115
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] 0.15 0.15 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.263 r_dihedral_angle_4_deg 19.111 r_sphericity_free 15.861 r_dihedral_angle_3_deg 14.429 r_sphericity_bonded 8.519 r_dihedral_angle_1_deg 5.502 r_rigid_bond_restr 2.355 r_angle_refined_deg 1.057 r_chiral_restr 0.081 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.263 r_dihedral_angle_4_deg 19.111 r_sphericity_free 15.861 r_dihedral_angle_3_deg 14.429 r_sphericity_bonded 8.519 r_dihedral_angle_1_deg 5.502 r_rigid_bond_restr 2.355 r_angle_refined_deg 1.057 r_chiral_restr 0.081 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1639 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 1
Software Software Software Name Purpose HKL-2000 data collection BALBES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling