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JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H4(1-15)R3me2s PEPTIDE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OX0 PDB ENTRY 2OX0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 SITTING DROPS, 277 K, 0.15 M POTASSIUM BROMIDE, 30 % W/V PEG 2000 MME, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.64 53.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.739 α = 90 b = 149.4 β = 90 c = 57.372 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 PIXEL DECTRIS PILATUS MIRRORS 2015-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 2.05 49.85 99.7 0.1 22.4 7.9 54997 2 33.84
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 2.05 2.12 99.8 1 2.5 8.1
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2OX0 2.05 49.854 1.34 54928 2709 99.47 0.2357 0.2342 0.2362 0.2551 0.2557 47.8
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] -0.74 -1.51 2.25
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.121 f_angle_d 0.779 f_chiral_restr 0.044 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5640 Nucleic Acid Atoms Solvent Atoms 391 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing