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Jumonji domain-containing protein 2B with crystallization epitope mutations L916G:R917A:A918D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LXL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277.15 2M ammonium sulfate
2% PEG400
0.1M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.71 66.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.85 α = 90 b = 88.85 β = 90 c = 143.86 γ = 120
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 2015-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 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 1.73 47.96 100 0.047 17.2 9.7 20481
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 1.73 1.78 1.593
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 1.8 18.58 20481 1035 100 0.2377 0.2368 0.2293 0.2553 0.2518 RANDOM 40.85
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] -0.8185 -0.8185 1.6369
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.73 t_omega_torsion 3.58 t_angle_deg 0.91 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1011 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 39
Software Software Software Name Purpose BUSTER refinement xia2 data reduction xia2 data scaling PHASER phasing