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R1EN(5-227)-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 7.3 283 2.0 M sodium acetate, 10 mM ammonium sulfate, 1% Jeffamine M600
Crystal Properties Matthews coefficient Solvent content 3.3 62.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.801 α = 90 b = 141.801 β = 90 c = 38.15 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 2015-10-12 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) 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 2.4 40 98.4 0.092 16.2 7.7 17861
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 2.4 2.49 100 0.742 2.5 7.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2EI9 2.4 36.46 15735 1324 98 0.193 0.189 0.1947 0.237 0.2377 RANDOM 51.19
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] -0.02 -0.01 -0.02 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.821 r_dihedral_angle_3_deg 17.692 r_dihedral_angle_4_deg 17.191 r_long_range_B_other 10.83 r_long_range_B_refined 10.828 r_dihedral_angle_1_deg 7.538 r_scangle_other 6.935 r_mcangle_it 5.908 r_mcangle_other 5.907 r_scbond_it 4.538
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.821 r_dihedral_angle_3_deg 17.692 r_dihedral_angle_4_deg 17.191 r_long_range_B_other 10.83 r_long_range_B_refined 10.828 r_dihedral_angle_1_deg 7.538 r_scangle_other 6.935 r_mcangle_it 5.908 r_mcangle_other 5.907 r_scbond_it 4.538 r_scbond_other 4.536 r_mcbond_it 3.735 r_mcbond_other 3.729 r_angle_refined_deg 1.283 r_angle_other_deg 0.906 r_chiral_restr 0.058 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 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 2288 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing