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JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16-35)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OX0 PDB ENRTY 2OX0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 VAPOUR DIFFUSION, SITTING DROP (PROTEIN:WELL, 1:2), 277 K, PACT PREMIER/G10: 0.02 M SODIUM/POTASSIUM PHOSPHATE, 0.1 M BIS TRIS PROPANE 7.5, 20 % W/V PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.64 53.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.711 α = 90 b = 149.74 β = 90 c = 57.508 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 6M MIRRORS 2013-07-13 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 1.81 60.07 99.9 0.1 9.9 6.9 79999 2 31.89
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 1.81 1.91 99.3 0.89 2 6.2
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 ENRTY 2OX0 1.81 60.072 1.33 79914 4010 99.85 0.1742 0.1724 0.1862 0.2082 0.1934
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.96 f_angle_d 1.321 f_chiral_restr 0.058 f_bond_d 0.01 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5646 Nucleic Acid Atoms Solvent Atoms 500 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALA data scaling PHASER phasing