☰ Navigation Tabs
R1EN(5-225)-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 7.5 283 2.0M sodium acetate, 10mM ammonium sulfate, 1% Jeffamine M600
Crystal Properties Matthews coefficient Solvent content 3.29 62.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.46 α = 90 b = 141.46 β = 90 c = 37.993 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 2015-07-06 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 40 100 0.174 10.2 7.5 17225
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 1.498 1.4 7.6
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 38.02 16373 880 99.9 0.208 0.206 0.2092 0.241 0.239 RANDOM 47.37
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] 0.24 0.12 0.24 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.152 r_dihedral_angle_4_deg 18.512 r_dihedral_angle_3_deg 18.358 r_long_range_B_refined 8.577 r_long_range_B_other 8.576 r_dihedral_angle_1_deg 7.199 r_scangle_other 5.812 r_mcangle_it 4.874 r_mcangle_other 4.874 r_scbond_it 3.692
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.152 r_dihedral_angle_4_deg 18.512 r_dihedral_angle_3_deg 18.358 r_long_range_B_refined 8.577 r_long_range_B_other 8.576 r_dihedral_angle_1_deg 7.199 r_scangle_other 5.812 r_mcangle_it 4.874 r_mcangle_other 4.874 r_scbond_it 3.692 r_scbond_other 3.691 r_mcbond_it 3.065 r_mcbond_other 3.063 r_angle_refined_deg 1.166 r_angle_other_deg 0.859 r_chiral_restr 0.054 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 2291 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing