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Crystal Structure of the 35-36 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 5.5 293.15 25-30% PEG 4000, 50 mM Sodium Cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K, pH 5.50
Crystal Properties Matthews coefficient Solvent content 2.07 40.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.817 α = 90 b = 49.786 β = 90 c = 123.147 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 ADSC QUANTUM 4 2004-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 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 1.55 19.511 98.5 0.054 20.02 44135 44135 27.02
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) 1.55 1.6 99.3 0.179 10.7
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 (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 1.55 19.511 48908 44135 2223 99.3 0.213 0.213 0.2611 0.227 0.2706 RANDOM 17.66
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] -0.43 0.12 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.79 r_dihedral_angle_4_deg 13.995 r_dihedral_angle_3_deg 12.598 r_dihedral_angle_1_deg 5.066 r_scangle_it 5.007 r_scbond_it 3.597 r_mcangle_it 2.013 r_mcbond_it 1.66 r_angle_refined_deg 1.391 r_angle_other_deg 0.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.79 r_dihedral_angle_4_deg 13.995 r_dihedral_angle_3_deg 12.598 r_dihedral_angle_1_deg 5.066 r_scangle_it 5.007 r_scbond_it 3.597 r_mcangle_it 2.013 r_mcbond_it 1.66 r_angle_refined_deg 1.391 r_angle_other_deg 0.796 r_mcbond_other 0.569 r_nbd_refined 0.313 r_symmetry_vdw_other 0.224 r_nbd_other 0.19 r_nbtor_refined 0.172 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.163 r_symmetry_vdw_refined 0.141 r_nbtor_other 0.083 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2451 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 3
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction JDirector data collection