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X-ray Crystal Structure of a Chemically Synthesized [L-Gln35]Ubiquitin with a Cubic Space Group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YIW pdb entry 1YIW, CHAIN B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.75 298 By mixing 2 ul of ubiquitin solution (20 mg/ml) and 0.5 ul of crystallization buffer solution. The crystallization buffer was prepared by mixing 3ml of HEPES buffer (0.1M), 3ml of poly(ethylene glycol) 3350 (25%, w/v), and 0.2ml of 1M cadmium acetate, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.92 57.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.578 α = 90 b = 106.578 β = 90 c = 106.578 γ = 90
Symmetry Space Group P 43 3 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 ADSC QUANTUM 210 MIRRORS 2004-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID
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 1.8 50 99.9 0.062 25.4 10.4 19783
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 1.8 1.86 99.9 0.49 1.8 9.5
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 (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 1YIW, CHAIN B 1.8 20 18714 1010 99.93 0.21 0.20652 0.205 0.2137 0.23608 0.2396 RANDOM 35.161
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 r_dihedral_angle_2_deg 35.404 r_dihedral_angle_4_deg 17.57 r_dihedral_angle_3_deg 13.117 r_dihedral_angle_1_deg 5.766 r_scangle_it 3.947 r_scbond_it 2.654 r_mcangle_it 1.646 r_angle_refined_deg 1.424 r_angle_other_deg 1.203 r_mcbond_it 0.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.404 r_dihedral_angle_4_deg 17.57 r_dihedral_angle_3_deg 13.117 r_dihedral_angle_1_deg 5.766 r_scangle_it 3.947 r_scbond_it 2.654 r_mcangle_it 1.646 r_angle_refined_deg 1.424 r_angle_other_deg 1.203 r_mcbond_it 0.986 r_nbd_refined 0.24 r_symmetry_vdw_refined 0.227 r_nbd_other 0.209 r_symmetry_vdw_other 0.186 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.1 r_metal_ion_refined 0.095 r_nbtor_other 0.079 r_chiral_restr 0.065 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_other_d r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_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 1174 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing