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Structural characterization for the nucleotide binding ability of subunit A with AMP-PNP 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, 0.1M acetate (pH 4.5), vapor diffusion, hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.29 62.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.391 α = 90 b = 128.391 β = 90 c = 105.019 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 mirrors 2008-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL12B2 1.00 SPring-8 BL12B2
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 2.4 50 99.7 0.068 32.12 14.4 34880 34852 65.87
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 2.4 2.49 100 0.459 4.17 14.1 3420
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 (All) 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 31.14 34880 34762 1737 99.66 0.248 0.221 0.219 0.2202 0.249 0.2308 RANDOM 64.471
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 38.076 r_dihedral_angle_4_deg 22.915 r_dihedral_angle_3_deg 19.671 r_dihedral_angle_1_deg 8.779 r_scangle_it 3.288 r_scbond_it 2.047 r_mcangle_it 1.711 r_angle_refined_deg 1.621 r_mcbond_it 0.99 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.076 r_dihedral_angle_4_deg 22.915 r_dihedral_angle_3_deg 19.671 r_dihedral_angle_1_deg 8.779 r_scangle_it 3.288 r_scbond_it 2.047 r_mcangle_it 1.711 r_angle_refined_deg 1.621 r_mcbond_it 0.99 r_nbtor_refined 0.31 r_symmetry_hbond_refined 0.23 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.222 r_xyhbond_nbd_refined 0.2 r_chiral_restr 0.112 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4145 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 67
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling