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Crystal structure of human JMJD2A in complex with fumarate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A7O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 0.1M BIS-TRIS PH 6.0 -- 0.15M AMMONIUM SULFATE -- 22% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.64 53.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.84 α = 90 b = 149.13 β = 90 c = 56.94 γ = 90
Symmetry Space Group P 21 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 PILATUS 6M 2015-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 2.35 29.83 99.8 0.07 16.8 6.6 36606 2.2
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 2.35 2.41 98.7 0.82 2.2 6.7
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 5A7O 2.348 29.798 1.34 36567 1741 99.71 0.2044 0.202 0.2067 0.2498 0.2519
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5555 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling DIMPLE phasing