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SP100 nuclear antigen with crystallization epitope mutations N816D:T820R
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PTB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277.15 0.2M ammonium sulfate
25% PEG3350
0.1M bis-tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.81 56.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.09 α = 90 b = 45.73 β = 102.37 c = 83.95 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 2015-10-18 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 1.35 82 96 0.041 14.6 3.5 100552
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 1.36 1.4 1.006
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.35 56.191 100552 5030 95.496 0.16 0.1584 0.1584 0.1852 0.1853 RANDOM 29.848
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] -0.07 0.183 -0.434 0.387
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.746 r_lrange_other 17.914 r_dihedral_angle_6_deg 15.353 r_scangle_it 13.835 r_scangle_other 13.832 r_dihedral_angle_3_deg 12.49 r_mcangle_it 10.351 r_mcangle_other 10.351 r_scbond_it 10.103 r_scbond_other 10.1
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.746 r_lrange_other 17.914 r_dihedral_angle_6_deg 15.353 r_scangle_it 13.835 r_scangle_other 13.832 r_dihedral_angle_3_deg 12.49 r_mcangle_it 10.351 r_mcangle_other 10.351 r_scbond_it 10.103 r_scbond_other 10.1 r_dihedral_angle_2_deg 9.791 r_mcbond_it 7.762 r_mcbond_other 7.736 r_dihedral_angle_1_deg 5.424 r_rigid_bond_restr 4.829 r_angle_refined_deg 1.783 r_angle_other_deg 0.696 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.219 r_nbd_other 0.2 r_nbtor_refined 0.175 r_symmetry_nbd_other 0.169 r_symmetry_nbd_refined 0.14 r_symmetry_xyhbond_nbd_refined 0.139 r_ncsr_local_group_1 0.119 r_chiral_restr 0.118 r_metal_ion_refined 0.106 r_symmetry_nbtor_other 0.068 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2868 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing