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Crystal structure of histone demethylase kdm2a-h3k36me3 complex with alpha-kg
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.1 M Na Citrate,
18-20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.01 38.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.797 α = 90 b = 84.615 β = 90 c = 170.077 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 CCD ADSC QUANTUM 315 2010-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C
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 1.65 86 96.6 0.062 0.049 4.6 88250 2.2 2.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 95.5 0.492 0.612 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 1.65 85.04 83656 88250 4648 99.23 0.19007 0.18816 0.1966 0.22668 0.2337 RANDOM 28.551
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] 0.25 1.56 -1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.459 r_dihedral_angle_4_deg 19.974 r_dihedral_angle_3_deg 14.116 r_dihedral_angle_1_deg 5.644 r_mcangle_it 2.109 r_scbond_it 1.811 r_mcbond_it 1.316 r_mcbond_other 1.316 r_angle_refined_deg 1.247 r_angle_other_deg 0.765
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.459 r_dihedral_angle_4_deg 19.974 r_dihedral_angle_3_deg 14.116 r_dihedral_angle_1_deg 5.644 r_mcangle_it 2.109 r_scbond_it 1.811 r_mcbond_it 1.316 r_mcbond_other 1.316 r_angle_refined_deg 1.247 r_angle_other_deg 0.765 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6696 Nucleic Acid Atoms Solvent Atoms 734 Heterogen Atoms 22
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling