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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 2OQ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 0.15M DL- malic acid
20% PEG3350
Crystal Properties Matthews coefficient Solvent content 4.15 70.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.04 α = 90 b = 91.04 β = 90 c = 102.26 γ = 120
Symmetry Space Group P 63 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 PIXEL DECTRIS PILATUS 6M 2015-12-09 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 1.96 62.47 100 0.079 20.3 18.9 18610
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 1.96 2.01 2.319
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 1.99 62.44 17759 831 100 0.2692 0.2686 0.2558 0.2795 0.2798 RANDOM 47.92
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] 2.9842 2.9842 -5.9683
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.25 t_omega_torsion 3.09 t_angle_deg 0.88 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 1003 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 30
Software Software Software Name Purpose BUSTER refinement xia2 data reduction xia2 data scaling PHASER phasing