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Structural characterization for the nucleotide binding ability of subunit A of the A1AO ATP synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VDZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 291 50% (v/v) MPD, 0.1 M acetate (pH 4.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.23 61.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.813 α = 90 b = 127.813 β = 90 c = 104.097 γ = 90
Symmetry Space Group P 43 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 CCD MARMOSAIC 225 mm CCD 2009-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 30 34274 34060
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 1VDZ 2.4 22.08 3 34274 32281 1717 99.55 0.21855 0.21641 0.2151 0.25939 0.2558 RANDOM 56.611
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.559 r_dihedral_angle_4_deg 22.153 r_dihedral_angle_3_deg 17.665 r_dihedral_angle_1_deg 6.411 r_scangle_it 3.478 r_scbond_it 2.032 r_mcangle_it 1.439 r_angle_refined_deg 1.426 r_mcbond_it 0.769 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.559 r_dihedral_angle_4_deg 22.153 r_dihedral_angle_3_deg 17.665 r_dihedral_angle_1_deg 6.411 r_scangle_it 3.478 r_scbond_it 2.032 r_mcangle_it 1.439 r_angle_refined_deg 1.426 r_mcbond_it 0.769 r_chiral_restr 0.102 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 4015 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling