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The structure of OsALKBH1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KHB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 MPD(2-methyl-1,3-propanediol), HEPES Sodium
Crystal Properties Matthews coefficient Solvent content 2.21 44.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.15 α = 90 b = 67.729 β = 99.89 c = 67.967 γ = 90
Symmetry Space Group C 1 2 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 CCD RAYONIX MX300HE 2017-01-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-BM 0.979 APS 17-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 50 99.9 0.047 0.03 32.6 3.4 20894
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 0.17 0.106 0.965 6.6 1.8
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 3KHB 1.8 50 19808 979 99.18 0.16351 0.16133 0.1727 0.20778 0.2118 RANDOM 24.393
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] -1.24 -0.02 -0.01 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.979 r_dihedral_angle_3_deg 12.794 r_dihedral_angle_4_deg 12.448 r_long_range_B_other 7.341 r_long_range_B_refined 7.338 r_dihedral_angle_1_deg 6.672 r_scangle_other 4.989 r_scbond_other 3.294 r_scbond_it 3.289 r_mcangle_it 2.537
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.979 r_dihedral_angle_3_deg 12.794 r_dihedral_angle_4_deg 12.448 r_long_range_B_other 7.341 r_long_range_B_refined 7.338 r_dihedral_angle_1_deg 6.672 r_scangle_other 4.989 r_scbond_other 3.294 r_scbond_it 3.289 r_mcangle_it 2.537 r_mcangle_other 2.537 r_mcbond_it 2.087 r_angle_refined_deg 2.051 r_mcbond_other 1.999 r_angle_other_deg 1.107 r_chiral_restr 0.163 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1710 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing