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X-ray Crystal Structure of a Chemically Synthesized [D-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 2.84 56.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.532 α = 90 b = 105.532 β = 90 c = 105.532 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 2004-11-22 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 2.2 50 99.5 0.033 47.3 8.5 10688
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 2.2 2.28 100 100 0.53 3.4 8.8
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 2.2 20 9591 1052 99.61 0.26 0.25443 0.24922 0.254 0.28286 0.2823 RANDOM 58.524
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 37.404 r_dihedral_angle_3_deg 17.643 r_dihedral_angle_4_deg 15.711 r_dihedral_angle_1_deg 7.171 r_scbond_it 2.935 r_scangle_it 2.838 r_angle_refined_deg 1.374 r_angle_other_deg 1.259 r_mcangle_it 1.194 r_mcbond_it 0.753
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.404 r_dihedral_angle_3_deg 17.643 r_dihedral_angle_4_deg 15.711 r_dihedral_angle_1_deg 7.171 r_scbond_it 2.935 r_scangle_it 2.838 r_angle_refined_deg 1.374 r_angle_other_deg 1.259 r_mcangle_it 1.194 r_mcbond_it 0.753 r_symmetry_vdw_refined 0.271 r_symmetry_vdw_other 0.233 r_nbd_refined 0.209 r_nbd_other 0.207 r_symmetry_hbond_refined 0.166 r_xyhbond_nbd_refined 0.16 r_nbtor_other 0.083 r_chiral_restr 0.068 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined 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 55 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing