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X-ray Crystal Structure of a Chemically Synthesized [D-Val35]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 2.9 57.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.152 α = 90 b = 106.152 β = 90 c = 106.152 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 MARRESEARCH MIRRORS 2004-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B APS 5ID-B
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 99.6 0.068 37.5 8.6 10927
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 99.1 0.66 3 8.7
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 10299 555 99.81 0.24 0.233 0.23071 0.2435 0.27808 0.2753 RANDOM 53.368
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 36.954 r_dihedral_angle_3_deg 17.041 r_dihedral_angle_4_deg 13.084 r_dihedral_angle_1_deg 6.926 r_scangle_it 3.671 r_scbond_it 2.335 r_angle_refined_deg 1.52 r_mcangle_it 1.454 r_angle_other_deg 1.291 r_mcbond_it 0.857
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.954 r_dihedral_angle_3_deg 17.041 r_dihedral_angle_4_deg 13.084 r_dihedral_angle_1_deg 6.926 r_scangle_it 3.671 r_scbond_it 2.335 r_angle_refined_deg 1.52 r_mcangle_it 1.454 r_angle_other_deg 1.291 r_mcbond_it 0.857 r_symmetry_vdw_refined 0.338 r_symmetry_vdw_other 0.291 r_nbd_refined 0.235 r_nbd_other 0.223 r_xyhbond_nbd_refined 0.211 r_symmetry_hbond_refined 0.134 r_xyhbond_nbd_other 0.089 r_nbtor_other 0.084 r_chiral_restr 0.075 r_metal_ion_refined 0.033 r_bond_refined_d 0.015 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_other_d r_nbtor_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 1170 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing