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Drosophila melanogaster JMJD7 (dmJMJD7) in complex with Mn and 2OG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NFO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.4 298 Sample: 16.0 mg/ml dmJMJD7 (in 50 mM Hepes-Na pH 7.5, 200 mM NaCl, 5% glycerol), 2.0 mM MnCl2 and 4.0 mM compound.
Reservoir: 0.1 M Bis-Tris pH 5.4, 0.3 M magnesium chloride, 0.1 M ammonium acetate (or alternatively, 0.1 M barium chloride), and 0.002 M manganese chloride.
Cryo-protection: 20% v/v ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 3.02 59.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.325 α = 90 b = 62.856 β = 109.06 c = 99.001 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 MIRRORS 2017-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.979450 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.64 50 99.8 0.076 0.085 0.041 0.996 18 4.8 103935 25.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.68 99.9 1.369 0.808 0.58 1.2 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 THROUGHOUT 5NFO 1.641 45.893 1.34 103792 4996 99.52 0.163 0.1618 0.1629 0.186 0.1852 44.2843
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 6.289 f_angle_d 1.119 f_chiral_restr 0.068 f_bond_d 0.011 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4920 Nucleic Acid Atoms Solvent Atoms 481 Heterogen Atoms 151
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing