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Structure of Thermus thermophilus cytochrome ba3 oxidase 360s after Xe depressurization
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XME
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 297 12-17% PEG 2000, 0-200mM KCl, 15-60mM bis-Tris pH 7.0, 6.5mM nonyl-B-D-glucopyranoside, vapor diffusion, hanging drop, temperature 297K
Crystal Properties Matthews coefficient Solvent content 3.23 61.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.92 α = 90 b = 113.92 β = 90 c = 177.35 γ = 90
Symmetry Space Group P 43 21 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 315 2009-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 4 95.85 99.9 0.135 18.9 27.2 10443
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4 4.22 100 0.438 0.438 1.7 27.9
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 1XME 4 95.85 10394 499 99.9 0.342 0.341 0.3343 0.373 0.3707 RANDOM 96.37
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] -0.64 -0.64 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.663 r_dihedral_angle_4_deg 17.55 r_dihedral_angle_3_deg 16.836 r_dihedral_angle_1_deg 5.302 r_angle_refined_deg 1.424 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.663 r_dihedral_angle_4_deg 17.55 r_dihedral_angle_3_deg 16.836 r_dihedral_angle_1_deg 5.302 r_angle_refined_deg 1.424 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5941 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 114
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction