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Human ubiquitin-conjugating enzyme E2 J2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AYZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 298 VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 1.91 35.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.07 α = 90 b = 48.014 β = 93.94 c = 91.032 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 CCD SBC-3 2005-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
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 30.84 95.8 0.067 23.67 3.3 23045 -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 2 2.07 85.6 0.238 4.74 2.9
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 1AYZ 2 30.84 23000 21287 1148 96.5 0.18962 0.18619 0.1857 0.25015 0.2498 RANDOM 36.137
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] -2.41 1.33 -3.06 5.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.384 r_dihedral_angle_4_deg 19.626 r_dihedral_angle_3_deg 15.647 r_dihedral_angle_1_deg 6.471 r_scangle_it 6.033 r_scbond_it 4.502 r_mcangle_it 3.567 r_mcbond_it 2.564 r_angle_refined_deg 1.642 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.384 r_dihedral_angle_4_deg 19.626 r_dihedral_angle_3_deg 15.647 r_dihedral_angle_1_deg 6.471 r_scangle_it 6.033 r_scbond_it 4.502 r_mcangle_it 3.567 r_mcbond_it 2.564 r_angle_refined_deg 1.642 r_nbtor_refined 0.318 r_symmetry_vdw_refined 0.278 r_symmetry_hbond_refined 0.253 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.188 r_chiral_restr 0.103 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_refined 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 2434 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing ARP/wARP model building