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Crystal structure of AMP-PNP bound A3B3 complex from Enterococcus hirae V-ATPase [bA3B3]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VR4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 296 26% PEG 3350, 0.1M HEPES, 0.2M Sodium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.58 52.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.11 α = 90 b = 124.13 β = 90 c = 245.33 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 2010-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 3.4 70.99 99.8 0.138 10.6 7.2 52024 52024 73.428
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 3.4 3.58 100 0.407 4.6 7.4 7506
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 3VR4 3.4 70.99 49208 49208 2651 99.6 0.19997 0.19997 0.19787 0.2004 0.23914 0.2369 RANDOM 92.677
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] -2.89 -2.48 5.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.838 r_dihedral_angle_3_deg 17.148 r_dihedral_angle_4_deg 14.722 r_dihedral_angle_1_deg 5.176 r_scangle_it 1.046 r_angle_refined_deg 1.032 r_scbond_it 0.608 r_mcangle_it 0.398 r_mcbond_it 0.205 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.838 r_dihedral_angle_3_deg 17.148 r_dihedral_angle_4_deg 14.722 r_dihedral_angle_1_deg 5.176 r_scangle_it 1.046 r_angle_refined_deg 1.032 r_scbond_it 0.608 r_mcangle_it 0.398 r_mcbond_it 0.205 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 24131 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 64
Software Software Software Name Purpose BSS data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling