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Ground state structure of F1-ATPase from bovine heart mitochondria (Bovine F1-ATPase crystallised in the absence of azide)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CK3 PDB ENTRY 2CK3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.2 50 MM TRIS-HCL PH 8.2, 200 MM NACL, 20 MM MGSO4, 250 UM AMP-PNP, 5 UM ADP, 0.004% (W/V) PHENYLMETHYLSULFONYL FLUORIDE AND 12% (W/V) POLYETHYLENE GLYCOL 6000
Crystal Properties Matthews coefficient Solvent content 2.29 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.61 α = 90 b = 123.13 β = 90 c = 261.76 γ = 90
Symmetry Space Group P 21 21 21
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 CCD MIRRORS 2006-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.9 20 72.8 0.06 15.9 3.1 194499 23.5
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 1.9 1.96 18.8 0.26 1.7 1.5
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 PDB ENTRY 2CK3 1.9 20 184625 9777 72.7 0.177 0.175 0.1776 0.22 0.2234 RANDOM 20.58
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] 0.27 1.06 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.956 r_dihedral_angle_4_deg 16.191 r_dihedral_angle_3_deg 14.577 r_scangle_it 7.651 r_scbond_it 5.468 r_dihedral_angle_1_deg 5.306 r_mcangle_it 3.427 r_mcbond_it 2.523 r_angle_refined_deg 1.119 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.956 r_dihedral_angle_4_deg 16.191 r_dihedral_angle_3_deg 14.577 r_scangle_it 7.651 r_scbond_it 5.468 r_dihedral_angle_1_deg 5.306 r_mcangle_it 3.427 r_mcbond_it 2.523 r_angle_refined_deg 1.119 r_nbtor_refined 0.298 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.17 r_xyhbond_nbd_refined 0.139 r_symmetry_hbond_refined 0.115 r_chiral_restr 0.073 r_bond_refined_d 0.008 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_refined 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23911 Nucleic Acid Atoms Solvent Atoms 2322 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing