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Ubiquitin-conjugating enzyme E2S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 3M Na formate, 0.1M bisTris, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.54 51.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.586 α = 90 b = 115.586 β = 90 c = 44.905 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2005-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.5418
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 1.93 30 100 0.074 29.03 6.8 26022 26022 -3
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 1.93 2 100 0.663 3.39 6.6 2575
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1JAT 1.93 27 26022 24678 1324 100 0.19509 0.19305 0.1947 0.23353 0.2386 RANDOM 25.812
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] 0.49 0.25 0.49 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.407 r_dihedral_angle_4_deg 21.65 r_dihedral_angle_3_deg 16.702 r_dihedral_angle_1_deg 6.26 r_scangle_it 5.037 r_scbond_it 3.07 r_mcangle_it 1.882 r_angle_refined_deg 1.625 r_mcbond_it 1.001 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.407 r_dihedral_angle_4_deg 21.65 r_dihedral_angle_3_deg 16.702 r_dihedral_angle_1_deg 6.26 r_scangle_it 5.037 r_scbond_it 3.07 r_mcangle_it 1.882 r_angle_refined_deg 1.625 r_mcbond_it 1.001 r_nbtor_refined 0.312 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.21 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.156 r_metal_ion_refined 0.116 r_chiral_restr 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2342 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing