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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 2GBM PDB ENTRY 2GBM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 279.15 25-30% PEG 4000, 50 mM Sodium Cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 279.15K
Crystal Properties Matthews coefficient Solvent content 1.87 34.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.773 α = 90 b = 45.773 β = 90 c = 111.549 γ = 120
Symmetry Space Group P 65 2 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 4 2005-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00808 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 1.6 37.35 100 0.094 16.5 19.17 9821 9821
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) 1.6 1.66 100 100 0.654 3.8 14.02
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 2GBM 1.6 37.35 9821 9768 469 99.96 0.20591 0.20591 0.20298 0.2106 0.26491 0.2757 RANDOM 20.801
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] 0.93 0.47 0.93 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.081 r_dihedral_angle_4_deg 16.802 r_dihedral_angle_3_deg 15.17 r_dihedral_angle_1_deg 6.517 r_scangle_it 5.992 r_scbond_it 5.035 r_sphericity_bonded 4.217 r_rigid_bond_restr 4.046 r_mcangle_it 2.798 r_mcbond_it 2.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.081 r_dihedral_angle_4_deg 16.802 r_dihedral_angle_3_deg 15.17 r_dihedral_angle_1_deg 6.517 r_scangle_it 5.992 r_scbond_it 5.035 r_sphericity_bonded 4.217 r_rigid_bond_restr 4.046 r_mcangle_it 2.798 r_mcbond_it 2.192 r_angle_refined_deg 1.947 r_angle_other_deg 1.036 r_mcbond_other 0.617 r_nbd_refined 0.25 r_symmetry_vdw_other 0.248 r_symmetry_hbond_refined 0.244 r_nbd_other 0.202 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.191 r_symmetry_vdw_refined 0.188 r_chiral_restr 0.126 r_nbtor_other 0.089 r_bond_refined_d 0.024 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 620 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction