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Crystal Structure of a Bovine Rabex-5 fragment complexed with ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FID PDB Entry 2FID
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 295 20-25% PEG 4000, 0.2M lithium sulfate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.79 55.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 192.2 α = 90 b = 44.42 β = 108.98 c = 69.17 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 ADSC QUANTUM 4 2005-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 1.2820 NSLS X12C
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 2.49 90.91 98.8 19257 19257
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 2.49 2.59 95.6
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 2FID 2.49 90.91 18271 18271 985 97.93 0.23003 0.23003 0.22821 0.2276 0.26347 0.2237 RANDOM 48.197
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] -1.17 -0.21 0.9 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.839 r_dihedral_angle_4_deg 16.682 r_dihedral_angle_3_deg 16.527 r_dihedral_angle_1_deg 4.75 r_scangle_it 1.077 r_angle_refined_deg 0.991 r_scbond_it 0.688 r_mcangle_it 0.426 r_nbtor_refined 0.295 r_mcbond_it 0.245
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.839 r_dihedral_angle_4_deg 16.682 r_dihedral_angle_3_deg 16.527 r_dihedral_angle_1_deg 4.75 r_scangle_it 1.077 r_angle_refined_deg 0.991 r_scbond_it 0.688 r_mcangle_it 0.426 r_nbtor_refined 0.295 r_mcbond_it 0.245 r_symmetry_vdw_refined 0.195 r_nbd_refined 0.178 r_xyhbond_nbd_refined 0.132 r_symmetry_hbond_refined 0.128 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3201 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing