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Crystal structure of the human UBR-box domain from UBR1 in complex with monomethylated arginine peptide.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NY1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 2.2 M (NH4)2SO4, 0.2 K/Na Tartrate
Crystal Properties Matthews coefficient Solvent content 1.73 28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.274 α = 90 b = 49.036 β = 90 c = 53.634 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 210 2010-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.9769 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.607 28.736 97.39 13.26 2.4 16360
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.607 1.63 86 1.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3NY1 1.607 28.736 1.37 16360 827 97.39 0.1505 0.1489 0.1504 0.1804 0.1808
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.992 f_angle_d 1.05 f_chiral_restr 0.062 f_bond_d 0.009 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1151 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PHASER phasing HKL-2000 data reduction