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Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36 peptide modified by UNC8015
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QX7 PDB entry 4QX7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 100 mM Tris-Cl, pH 8.5, 150 mM lithium sulfate, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.903 α = 90 b = 87.054 β = 90 c = 176.177 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2022-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.98 88.09 97.35 0.19 0.22 0.09 0.991 6.48 6.3 58130 36.82
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.03 98.3 0.674 6.7
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 4QX7 1.98 88.09 55260 2914 97.42 0.18552 0.18285 0.1905 0.23701 0.2417 RANDOM 30.473
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] 0.64 1.56 -2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.424 r_dihedral_angle_4_deg 21.838 r_dihedral_angle_3_deg 14.7 r_long_range_B_refined 7.166 r_long_range_B_other 7.077 r_dihedral_angle_1_deg 6.297 r_scangle_other 5.55 r_scbond_it 3.622 r_scbond_other 3.622 r_mcangle_other 3.255
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.424 r_dihedral_angle_4_deg 21.838 r_dihedral_angle_3_deg 14.7 r_long_range_B_refined 7.166 r_long_range_B_other 7.077 r_dihedral_angle_1_deg 6.297 r_scangle_other 5.55 r_scbond_it 3.622 r_scbond_other 3.622 r_mcangle_other 3.255 r_mcangle_it 3.252 r_mcbond_it 2.329 r_mcbond_other 2.329 r_angle_refined_deg 1.764 r_angle_other_deg 1.034 r_chiral_restr 0.105 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.006 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 6675 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing