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Crystal Structure of the 9-10 8 Glycine Insertion Mutant of Ubiquitin.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ PDB ENTRY 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 279.15 27-32% PEG 4000, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 279.15K
Crystal Properties Matthews coefficient Solvent content 1.736554 29.170057
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.124 α = 90 b = 53.035 β = 90 c = 87.268 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 NOIR-1 180 cm lens focused ccd 2004-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.12711 ALS 4.2.2
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 1.35 33.691 97.8 0.068 10.8 4.98 28499 27867
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) 1.35 1.4 90.6 90.6 0.503 2.4 4.37 2511
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 1UBQ 1.35 33.691 28499 27864 1405 97.78 0.18998 0.18998 0.18805 0.3452 0.22589 0.3608 RANDOM 33.353
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] -0.59 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.53 r_dihedral_angle_4_deg 20.878 r_dihedral_angle_3_deg 13.379 r_dihedral_angle_1_deg 6.042 r_scangle_it 4.494 r_scbond_it 3.215 r_sphericity_bonded 2.737 r_mcangle_it 1.946 r_rigid_bond_restr 1.921 r_mcbond_it 1.657
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.53 r_dihedral_angle_4_deg 20.878 r_dihedral_angle_3_deg 13.379 r_dihedral_angle_1_deg 6.042 r_scangle_it 4.494 r_scbond_it 3.215 r_sphericity_bonded 2.737 r_mcangle_it 1.946 r_rigid_bond_restr 1.921 r_mcbond_it 1.657 r_angle_refined_deg 1.416 r_angle_other_deg 0.86 r_mcbond_other 0.646 r_symmetry_vdw_other 0.243 r_symmetry_vdw_refined 0.207 r_nbd_refined 0.206 r_nbd_other 0.188 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.165 r_symmetry_hbond_refined 0.147 r_chiral_restr 0.083 r_nbtor_other 0.08 r_xyhbond_nbd_other 0.04 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1259 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms
Software Software Software Name Purpose d*TREK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection