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Structure of KIAA1718 Jumonji domain in complex with N-oxalylglycine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KV6 PDB entry 3KV6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 289 17-20% (v/v) polyethylene glycol 5000 MME, 0.2 M CaCl2, and 0.1 M BisTris pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.78 55.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.3 α = 90 b = 78.3 β = 90 c = 289.1 γ = 120
Symmetry Space Group P 61 2 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 MARMOSAIC 225 mm CCD 2008-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
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 2.69 33.67 98.3 0.085 13.3 14.4 15320 37.7
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) 2.69 2.79 86.3 0.394 2.6 8 1303
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3KV6 2.69 33.67 14477 711 93.4 0.216 0.2207 0.267 RANDOM 54.9
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] 10.87 10.87 -21.73
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_scangle_it 3.07 c_mcangle_it 2.22 c_scbond_it 1.98 c_angle_deg 1.3 c_mcbond_it 1.3 c_improper_angle_d 0.78 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2941 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 14
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling