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Jumonji domain-containing protein 2A with crystallization epitope mutations A91T:T93S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M lithium sulfate,
25% PEG3350,
0.1M bis-tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.76 55.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.7 α = 90 b = 90.78 β = 107.19 c = 90.67 γ = 90
Symmetry Space Group C 1 2 1
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 2014-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.88 40.449 99.5 0.997 12.5 3.4 73694
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.93 0.783
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.88 40.449 73693 3667 99.447 0.187 0.1854 0.1854 0.2223 0.2224 39.163
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] 1.908 0.588 1.152 -2.873
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.517 r_dihedral_angle_3_deg 13.594 r_dihedral_angle_2_deg 8.906 r_lrange_other 8.859 r_lrange_it 8.858 r_scangle_it 7.379 r_scangle_other 7.378 r_dihedral_angle_1_deg 7.08 r_mcangle_it 6.1 r_mcangle_other 6.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.517 r_dihedral_angle_3_deg 13.594 r_dihedral_angle_2_deg 8.906 r_lrange_other 8.859 r_lrange_it 8.858 r_scangle_it 7.379 r_scangle_other 7.378 r_dihedral_angle_1_deg 7.08 r_mcangle_it 6.1 r_mcangle_other 6.1 r_scbond_it 5.403 r_scbond_other 5.402 r_mcbond_other 4.844 r_mcbond_it 4.843 r_angle_refined_deg 2.053 r_angle_other_deg 0.863 r_symmetry_xyhbond_nbd_refined 0.685 r_symmetry_nbd_refined 0.584 r_metal_ion_refined 0.269 r_xyhbond_nbd_other 0.23 r_nbd_refined 0.208 r_nbtor_refined 0.183 r_nbd_other 0.183 r_symmetry_nbd_other 0.167 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.114 r_ncsr_local_group_1 0.101 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.03 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5498 Nucleic Acid Atoms Solvent Atoms 446 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing