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Crystal Structure of T5 D15 Protein Co-crystallized with Metal Ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UT5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 280 Bis-Tris propane, PEG 3350, MgCl2, NaI
Crystal Properties Matthews coefficient Solvent content 2.33 47.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.38 α = 66.53 b = 58.38 β = 79.48 c = 59.72 γ = 73.71
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2010-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9795 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.482 54.602 93.7 0.057 0.069 0.039 11.4 3 87441 87441
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.482 1.56 92.6 0.491 0.491 0.341 1.3 3 12624
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 (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 1UT5 1.482 54.6 83074 4367 93.72 0.1433 0.1406 0.1398 0.1958 0.1943 RANDOM 19.889
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] -0.04 0.15 -0.25 0.15 -0.02 -0.08
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.872 r_dihedral_angle_2_deg 32.477 r_dihedral_angle_4_deg 15.702 r_sphericity_bonded 15.263 r_dihedral_angle_3_deg 11.796 r_dihedral_angle_1_deg 5.014 r_mcangle_it 4.333 r_mcbond_it 3.928 r_mcbond_other 3.921 r_rigid_bond_restr 2.194
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.872 r_dihedral_angle_2_deg 32.477 r_dihedral_angle_4_deg 15.702 r_sphericity_bonded 15.263 r_dihedral_angle_3_deg 11.796 r_dihedral_angle_1_deg 5.014 r_mcangle_it 4.333 r_mcbond_it 3.928 r_mcbond_other 3.921 r_rigid_bond_restr 2.194 r_angle_refined_deg 1.324 r_angle_other_deg 1.007 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4380 Nucleic Acid Atoms Solvent Atoms 559 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing