☰ Navigation Tabs
Structure of JMJD6 complexd with ALPHA-KETOGLUTARATE and Fab Fragment.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LD8 PDB entries 3LD8, JMJD6, and Fab Fragment
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 277 0.1 M Bis(2-hydroxyethyl)-amino-tris(hydroxymethyl)-methane, 2.1 M Ammonium Sulphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 5.02 75.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.381 α = 90 b = 138.381 β = 90 c = 183.622 γ = 90
Symmetry Space Group P 41 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 CCD ADSC QUANTUM 315 2005-10-10 M SINGLE WAVELENGTH 2 1 x-ray CCD ADSC QUANTUM 315 2005-10-10
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1 2 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.61 99 89 54702 48696 66.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entries 3LD8, JMJD6, and Fab Fragment 2.7 47.28 55302 40520 2024 81.7 0.25 0.25 0.2493 0.285 0.2847 RANDOM 83.5
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] 10.72 10.72 -21.44
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.9 c_mcangle_it 7.84 c_mcbond_it 5.97 c_scangle_it 3.15 c_scbond_it 2.11 c_angle_deg 1.5 c_improper_angle_d 1.02 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.9 c_mcangle_it 7.84 c_mcbond_it 5.97 c_scangle_it 3.15 c_scbond_it 2.11 c_angle_deg 1.5 c_improper_angle_d 1.02 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6072 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 138
Software Software Software Name Purpose HKL-2000 data collection CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing