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R1EN(5-223)-ubiquitin fusion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EI9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 283 2.0M sodium acetate, 10mM ammonium sulfate, 1% Jeffamine M600,
Crystal Properties Matthews coefficient Solvent content 3.29 62.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.206 α = 90 b = 141.206 β = 90 c = 37.905 γ = 120
Symmetry Space Group P 3 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 90 CCD RAYONIX MX300HE 2015-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.7 40 96 0.131 0.144 0.06 0.994 11.4 11.2 45813
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 68.7 0.866 0.961 0.408 0.76 2.4 10.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2ei9 1.7 36.23 43652 2156 95.83 0.19245 0.19105 0.22001 0.243 RANDOM 31.738
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] 0.19 0.1 0.19 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.153 r_dihedral_angle_4_deg 17.041 r_dihedral_angle_3_deg 16.981 r_long_range_B_refined 8.021 r_long_range_B_other 8.019 r_dihedral_angle_1_deg 7.391 r_scangle_other 6.079 r_mcangle_it 4.142 r_mcangle_other 4.142 r_scbond_it 4.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.153 r_dihedral_angle_4_deg 17.041 r_dihedral_angle_3_deg 16.981 r_long_range_B_refined 8.021 r_long_range_B_other 8.019 r_dihedral_angle_1_deg 7.391 r_scangle_other 6.079 r_mcangle_it 4.142 r_mcangle_other 4.142 r_scbond_it 4.041 r_scbond_other 4.039 r_mcbond_it 2.908 r_mcbond_other 2.903 r_angle_refined_deg 1.595 r_angle_other_deg 1.022 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2280 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing