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Structure of an Arabidopsis E2 / Membrane-anchored Ubiquitin-fold Protein Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NOB PDB ENTRY ID 3NOB, 1QCQ experimental model PDB 1QCQ PDB ENTRY ID 3NOB, 1QCQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 280 3.0 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 3.86 68.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.716 α = 90 b = 135.716 β = 90 c = 202.134 γ = 120
Symmetry Space Group P 63 2 2
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 RAYONIX MX-300 2013-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97934 APS 23-ID-D
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 2.8 50 99.8 0.07 30 7.2 27721 -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 2.8 2.85 100 1 1.95 7.3
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 PDB ENTRY ID 3NOB, 1QCQ 2.8 10 25543 1346 96.79 0.22301 0.22119 0.2284 0.25682 0.2581 RANDOM 75.553
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] 0.25 0.13 0.25 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.677 r_dihedral_angle_3_deg 21.194 r_dihedral_angle_4_deg 18.594 r_long_range_B_refined 13.732 r_long_range_B_other 13.732 r_scangle_other 11.423 r_mcangle_it 8.867 r_mcangle_other 8.866 r_scbond_it 7.956 r_dihedral_angle_1_deg 7.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.677 r_dihedral_angle_3_deg 21.194 r_dihedral_angle_4_deg 18.594 r_long_range_B_refined 13.732 r_long_range_B_other 13.732 r_scangle_other 11.423 r_mcangle_it 8.867 r_mcangle_other 8.866 r_scbond_it 7.956 r_dihedral_angle_1_deg 7.938 r_scbond_other 7.776 r_mcbond_it 6.228 r_mcbond_other 6.226 r_angle_refined_deg 1.544 r_angle_other_deg 0.813 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 3720 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing