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Jumonji domain-containing protein 2A with crystallization epitope mutations Q953E:A958D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GD4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2M ammonium sulfate,
0.1M bis-tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 3.95 68.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.1 α = 90 b = 136.1 β = 90 c = 136.1 γ = 90
Symmetry Space Group I 41 3 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 0.916 Diamond I04-1
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 1.58 96.23 100 1 25.9 38.2 29690
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 1.58 1.62 0.803
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.59 55.624 29114 1375 99.99 0.162 0.161 0.1795 0.1551 28.161
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 r_lrange_it 23.34 r_lrange_other 22.499 r_scangle_it 16.631 r_scangle_other 16.172 r_dihedral_angle_6_deg 15.073 r_dihedral_angle_3_deg 12.701 r_scbond_it 11.836 r_scbond_other 11.422 r_dihedral_angle_2_deg 9.383 r_mcangle_other 9.375
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 23.34 r_lrange_other 22.499 r_scangle_it 16.631 r_scangle_other 16.172 r_dihedral_angle_6_deg 15.073 r_dihedral_angle_3_deg 12.701 r_scbond_it 11.836 r_scbond_other 11.422 r_dihedral_angle_2_deg 9.383 r_mcangle_other 9.375 r_mcangle_it 9.364 r_dihedral_angle_1_deg 7.656 r_mcbond_it 6.652 r_mcbond_other 6.607 r_rigid_bond_restr 4.862 r_angle_refined_deg 1.977 r_angle_other_deg 0.839 r_xyhbond_nbd_refined 0.207 r_nbd_refined 0.178 r_symmetry_nbd_other 0.165 r_nbtor_refined 0.161 r_symmetry_nbd_refined 0.142 r_symmetry_xyhbond_nbd_refined 0.133 r_chiral_restr 0.107 r_nbd_other 0.098 r_symmetry_nbtor_other 0.073 r_symmetry_xyhbond_nbd_other 0.05 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 931 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing