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Crystal structure of yeast mitochondrial F1-ATPase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E1Q PDB ENTRY 1E1Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 277 5.5% PEG 6000, 10% glycerol, 4% methanol, 0.05M sodium acetate, 0.5mM nickel sulphate, 0.5mM AMP/PNP, 0.025 mM ADP, 2mM magnesium chloride, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.75 55.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.524 α = 90 b = 294.132 β = 101.67 c = 190.432 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 225 mm CCD 2003-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 1.0 APS 5ID-B
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 2.6 30 94 0.074 11.7 3.6 346124
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 2.6 2.7 94 0.406 2.6 2 36073
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB ENTRY 1E1Q 2.8 20 2 293909 286907 5938 99.94 0.20731 0.20659 0.211 0.24412 0.2445 RANDOM 70.39
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] 1.52 -0.91 -0.42 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.257 r_dihedral_angle_4_deg 18.689 r_dihedral_angle_3_deg 16.083 r_scangle_it 6.462 r_dihedral_angle_1_deg 5.626 r_scbond_it 4.401 r_mcangle_it 2.828 r_mcbond_it 1.645 r_angle_refined_deg 1.346 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.257 r_dihedral_angle_4_deg 18.689 r_dihedral_angle_3_deg 16.083 r_scangle_it 6.462 r_dihedral_angle_1_deg 5.626 r_scbond_it 4.401 r_mcangle_it 2.828 r_mcbond_it 1.645 r_angle_refined_deg 1.346 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.276 r_symmetry_vdw_refined 0.237 r_nbd_refined 0.216 r_metal_ion_refined 0.139 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 72173 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 485
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing