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Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Dsk2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QIZ PDB ENTRY 2QIZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 298 16-18% PEG 3500
200 mM Tripotassium citrate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.03 59.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.13 α = 90 b = 125.7 β = 90 c = 181.21 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315r 2009-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.976 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 73.501 98.6 0.062 0.062 12.9 3.8 58089 58089
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 95.1 0.509 0.509 2.2 3.5 58089
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 (All) 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 2QIZ 2.4 73.5 58038 58038 2951 98.26 0.21 0.21 0.206 0.2148 0.27 0.2791 RANDOM 42.881
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] 0.81 -0.05 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.293 r_dihedral_angle_3_deg 19.834 r_dihedral_angle_4_deg 18.844 r_dihedral_angle_1_deg 6.277 r_scangle_it 5.016 r_scbond_it 3.356 r_mcangle_it 2.113 r_angle_refined_deg 1.61 r_mcbond_it 1.13 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.293 r_dihedral_angle_3_deg 19.834 r_dihedral_angle_4_deg 18.844 r_dihedral_angle_1_deg 6.277 r_scangle_it 5.016 r_scbond_it 3.356 r_mcangle_it 2.113 r_angle_refined_deg 1.61 r_mcbond_it 1.13 r_chiral_restr 0.112 r_bond_refined_d 0.015 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8269 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 17
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MxCuBE data collection