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STRUCTURE OF JMJD2A COMPLEXED WITH INHIBITOR 10A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OQ6 PDB ENTRY 2OQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 PROTEIN STOCK 11MG/ML JMJD2A, 10MM HEPES PH7.5, 500MM NACL, 5% GLYCEROL, 0.75MM INHIBITOR 10A. RESERVOIR: 0.1M CITRATE PH5.5, 18.5% PEG3350, 4MM NICL2. 1:1 PROTEIN/RESERVOIR
Crystal Properties Matthews coefficient Solvent content 2.68 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.33 α = 90 b = 148.97 β = 90 c = 57.11 γ = 90
Symmetry Space Group P 21 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 100 CCD ADSC CCD MIRRORS 2009-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.6 49.75 99.9 0.13 12.2 6.64 27338 47.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.74 99.6 0.59 3.37 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 2OQ6 2.6 47.97 26102 1191 99.81 0.18104 0.17799 0.1857 0.24758 0.25 RANDOM 38.27
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] -0.58 -0.27 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.143 r_dihedral_angle_4_deg 19.524 r_dihedral_angle_3_deg 18.486 r_dihedral_angle_1_deg 6.69 r_scangle_it 4.097 r_scbond_it 2.561 r_angle_refined_deg 1.649 r_mcangle_it 1.489 r_mcbond_it 0.746 r_chiral_restr 0.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.143 r_dihedral_angle_4_deg 19.524 r_dihedral_angle_3_deg 18.486 r_dihedral_angle_1_deg 6.69 r_scangle_it 4.097 r_scbond_it 2.561 r_angle_refined_deg 1.649 r_mcangle_it 1.489 r_mcbond_it 0.746 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 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_other r_mcangle_other r_scbond_other 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 5697 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing