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Intermediate position of ATP on its trail to the binding pocket inside the subunit B mutant R416W of the energy converter A1Ao ATP synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C61 PDB ENTRY 2C61
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 291 15% glycerol, 20% PEG 400, 2mM Mg2+ ATP, 0.1M Sodium Chloride, 0.1M Sodium citrate (pH 5.0), pH 5.00, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.23 44.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.473 α = 90 b = 96.094 β = 90 c = 130.275 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 QUANTUM 210 MIRRORS 2007-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 NSRRC BL13C1
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 30 99.4 0.088 13.8084 3.3 62523 11.7
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) 2 2.07 98.7 0.594 2.264 3.1
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 (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 2C61 2.1 26.96 73949 51314 5244 94.1 0.189 0.189 0.1857 0.237 0.2334 RANDOM 31
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] 11.66 -4.41 -7.26
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_scangle_it 3.335 c_mcangle_it 2.246 c_scbond_it 2.192 c_improper_angle_d 2.17 c_angle_deg 1.8 c_mcbond_it 1.424 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_scangle_it 3.335 c_mcangle_it 2.246 c_scbond_it 2.192 c_improper_angle_d 2.17 c_angle_deg 1.8 c_mcbond_it 1.424 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6692 Nucleic Acid Atoms Solvent Atoms 828 Heterogen Atoms 57
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing CNS refinement PDB_EXTRACT data extraction ADSC data collection