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Structure of the reduced form 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 7 297 Peg 2000, Bis-tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.74 55.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.631 α = 90 b = 115.631 β = 90 c = 149.169 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 Q315R ADSC Quantum-315R CCD Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing). 2007-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.979 SSRL BL7-1
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 2.55 20 99.7 0.05 6.3 3.9 33534 2 2
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 2.55 2.62 100 0.763 0.9 4.1
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 2.8 20 24159 1274 99.8 0.19959 0.19656 0.198 0.257 0.2625 RANDOM 89.502
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 -0.28 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.335 r_dihedral_angle_3_deg 21.118 r_dihedral_angle_4_deg 20.037 r_dihedral_angle_1_deg 7.895 r_scangle_it 4.565 r_scbond_it 3.418 r_mcangle_it 2.756 r_angle_refined_deg 2.153 r_mcbond_it 1.68 r_symmetry_vdw_refined 0.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.335 r_dihedral_angle_3_deg 21.118 r_dihedral_angle_4_deg 20.037 r_dihedral_angle_1_deg 7.895 r_scangle_it 4.565 r_scbond_it 3.418 r_mcangle_it 2.756 r_angle_refined_deg 2.153 r_mcbond_it 1.68 r_symmetry_vdw_refined 0.359 r_nbtor_refined 0.327 r_nbd_refined 0.266 r_xyhbond_nbd_refined 0.19 r_chiral_restr 0.135 r_symmetry_hbond_refined 0.09 r_metal_ion_refined 0.087 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5966 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 195
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling