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An unexpected outcome of surface-engineering an integral membrane protein: Improved crystallization of cytochrome ba3 oxidase from Thermus thermophilus
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 VAPOR DIFFUSION, SITTING DROP 7 291 7% PEK 2K, 50 mM KCl, 20 mM Bis-Tris pH 7.0, 6.5 mM n-nonyl-beta-D-glucopyranoside, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.88 57.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.19 α = 90 b = 115.19 β = 90 c = 149.14 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 mirrors 2007-04-06 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 3.25 20 82.8 0.032 18.1 3.3 13540 13540
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 3.25 3.43 82.8 0.618 1.2 3.8 2076
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 1XME 3.25 19.98 13540 13540 780 77.18 0.3067 0.21982 0.215 0.1887 0.307 0.2983 RANDOM 44.113
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] 0.45 0.45 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.562 r_dihedral_angle_3_deg 25.554 r_dihedral_angle_4_deg 21.716 r_scangle_it 11.779 r_dihedral_angle_1_deg 10.065 r_scbond_it 8.537 r_mcangle_it 5.878 r_mcbond_it 3.549 r_angle_refined_deg 2.622 r_nbtor_refined 0.356
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.562 r_dihedral_angle_3_deg 25.554 r_dihedral_angle_4_deg 21.716 r_scangle_it 11.779 r_dihedral_angle_1_deg 10.065 r_scbond_it 8.537 r_mcangle_it 5.878 r_mcbond_it 3.549 r_angle_refined_deg 2.622 r_nbtor_refined 0.356 r_symmetry_vdw_refined 0.343 r_nbd_refined 0.331 r_xyhbond_nbd_refined 0.233 r_chiral_restr 0.153 r_metal_ion_refined 0.141 r_symmetry_hbond_refined 0.122 r_bond_refined_d 0.023 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5966 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 111
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection MOSFLM data reduction SCALA data scaling PHASES phasing