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Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000.
Co-substrate analog NOG and H3R9 peptide were co-crystallised with the protein.
Crystal Properties Matthews coefficient Solvent content 2.48 50.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.44 α = 90 b = 103.41 β = 99.63 c = 144.52 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 100 PIXEL DECTRIS PILATUS 6M-F 2017-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.33 44.27 99.7 0.18 0.984 8.6 6.5 72206 52.57
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.33 2.39 100 1.153 0.56 1.6 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 2oq6 2.33 43.16 72205 3503 99.7 0.252 0.251 0.2579 0.28 0.2849 RANDOM 44.44
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] 2.7905 -7.6188 3.6331 -6.4236
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.67 t_omega_torsion 2.73 t_angle_deg 1.05 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.67 t_omega_torsion 2.73 t_angle_deg 1.05 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10996 Nucleic Acid Atoms Solvent Atoms 465 Heterogen Atoms 48
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing