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Structure of Surface-engineered Cytochrome ba3 Oxidase from Thermus thermophilus under Xenon Pressure, 100psi 5min
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XME PDB ENTRY 1XME
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 297 6-9% PEG 2000, 50mM KCl, 7.5-30mM bis-Tris pH 7.0, 6.5mM nonyl-B-D-glucopyranoside , VAPOR DIFFUSION, temperature 297K
Crystal Properties Matthews coefficient Solvent content 3.21 61.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.726 α = 90 b = 119.726 β = 90 c = 153.535 γ = 90
Symmetry Space Group P 41 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 Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing) 2007-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.979 SSRL BL9-1
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 3.37 27.16 99.7 0.068 8.1 4.5 16390 16341 108.222
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) 3.37 3.55 100 0.463 1.8 4.8 2339
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-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 1XME 3.37 26.96 16297 16329 823 99.84 0.2922 0.2676 0.3355 0.3236 RANDOM 85.48
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 -0.04 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.125 r_dihedral_angle_3_deg 19.271 r_dihedral_angle_4_deg 18.676 r_dihedral_angle_1_deg 5.323 r_angle_refined_deg 1.304 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.277 r_metal_ion_refined 0.211 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.125 r_dihedral_angle_3_deg 19.271 r_dihedral_angle_4_deg 18.676 r_dihedral_angle_1_deg 5.323 r_angle_refined_deg 1.304 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.277 r_metal_ion_refined 0.211 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.127 r_symmetry_hbond_refined 0.099 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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 5907 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC phasing CNS phasing Coot model building CNS refinement