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Drosophila melanogaster JMJD7 (dmJMJD7) in complex with Mn and N-oxalyl-D-phenylalanine (NOFD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YXG
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 2.5 50.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.02 α = 90 b = 65.16 β = 100.77 c = 99.22 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 2017-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97951 Diamond I04
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 2.2 40.42 99.8 0.138 0.154 0.067 0.995 9.9 5.1 35134 34.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 99.7 1.229 1.364 0.582 0.559 5.2
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 7YXG 2.2 40.418 1.34 35112 1758 99.74 0.1906 0.1885 0.2018 0.2298 0.2369 53.3569
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 15.114 f_angle_d 0.654 f_chiral_restr 0.046 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4834 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 140
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing