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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 1EXN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 280 PACT H2: 0.2M Na bromide, 0.1M Bis Tris propane pH 8.5, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.32 46.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.831 α = 66.88 b = 58.591 β = 79.4 c = 59.729 γ = 73.78
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 2011-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97836 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 1.5 54.735 93.1 0.083 0.093 0.042 10.5 3.8 83343 83343
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 1.5 1.58 90.4 0.322 0.322 0.296 1.6 2.2 11812
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 1EXN 1.5 38.35 79049 4123 92.77 0.1501 0.1477 0.1462 0.1967 0.195 RANDOM 19.387
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] 0.28 0.37 0.58 0.12 -0.21 -0.2
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.009 r_dihedral_angle_2_deg 32.03 r_sphericity_bonded 27.767 r_dihedral_angle_4_deg 13.935 r_rigid_bond_restr 11.794 r_dihedral_angle_3_deg 11.609 r_dihedral_angle_1_deg 5.294 r_mcangle_it 3.066 r_mcbond_it 2.778 r_mcbond_other 2.729
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.009 r_dihedral_angle_2_deg 32.03 r_sphericity_bonded 27.767 r_dihedral_angle_4_deg 13.935 r_rigid_bond_restr 11.794 r_dihedral_angle_3_deg 11.609 r_dihedral_angle_1_deg 5.294 r_mcangle_it 3.066 r_mcbond_it 2.778 r_mcbond_other 2.729 r_angle_other_deg 1.815 r_angle_refined_deg 1.329 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4349 Nucleic Acid Atoms Solvent Atoms 598 Heterogen Atoms 16
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing