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crystal structure of human JMJD2D in complex with 2,4-PDCA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 27% PEG3350 -- 0.1M HEPES PH 7.0 -- 0.25M AMMONIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 2.47 50.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.91 α = 90 b = 71.91 β = 90 c = 151.06 γ = 90
Symmetry Space Group P 43 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 PIXEL 2012-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.29 33.43 100 0.07 15.9 7.2 99689 -3 12.99
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 1.29 1.33 100 0.68 2.8 6.8
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 NONE 1.292 33.435 1.89 99584 5006 99.94 0.1361 0.1348 0.1376 0.1613 0.1622
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 12.291 f_angle_d 1.079 f_chiral_restr 0.049 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2660 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling