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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, 0.1M Sodium Chloride, 0.1M Sodium citrate (pH 5.0), VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.21 44.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.052 α = 90 b = 96.094 β = 90 c = 129.941 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 315 mirrors 2007-01-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.00 NSRRC BL13B1
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 2.8 50 87 0.13 8.4 5.9 20054
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) 2.8 2.9 60.6 0.395 4.8
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2C61 2.81 34.73 19988 1033 86.9 0.274 0.271 0.269 0.33 0.3372 79.45
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] 0.14 0.11 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.656 r_dihedral_angle_3_deg 21.035 r_dihedral_angle_4_deg 14.095 r_dihedral_angle_1_deg 7.295 r_angle_refined_deg 1.36 r_scangle_it 0.894 r_mcangle_it 0.609 r_scbond_it 0.537 r_mcbond_it 0.335 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.656 r_dihedral_angle_3_deg 21.035 r_dihedral_angle_4_deg 14.095 r_dihedral_angle_1_deg 7.295 r_angle_refined_deg 1.36 r_scangle_it 0.894 r_mcangle_it 0.609 r_scbond_it 0.537 r_mcbond_it 0.335 r_nbtor_refined 0.31 r_nbd_refined 0.235 r_symmetry_vdw_refined 0.202 r_xyhbond_nbd_refined 0.184 r_chiral_restr 0.103 r_symmetry_hbond_refined 0.028 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6512 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing PDB_EXTRACT data extraction REFMAC refinement