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Crystal structure of nucleotide-free A3B3 complex from Enterococcus hirae V-ATPase [eA3B3]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GQB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 296 24% PEG 3350, 0.1M Tris, 0.2M Ammonium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.64 53.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.8 α = 90 b = 121.5 β = 90.06 c = 128.26 γ = 90
Symmetry Space Group P 1 21 1
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 2.8 44.18 99.3 0.068 11.6 3.7 91463 91463 77.186
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 2.8 2.95 99.4 0.349 3.5 3.7 13339
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 3GQB 2.8 44.18 86877 86877 4572 99.28 0.20061 0.20061 0.19837 0.1982 0.24293 0.242 RANDOM 76.336
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] 0.27 0.63 1.48 -1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.064 r_dihedral_angle_3_deg 18.755 r_dihedral_angle_4_deg 17.303 r_dihedral_angle_1_deg 6.085 r_scangle_it 3.006 r_scbond_it 1.804 r_angle_refined_deg 1.333 r_mcangle_it 0.922 r_mcbond_it 0.457 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.064 r_dihedral_angle_3_deg 18.755 r_dihedral_angle_4_deg 17.303 r_dihedral_angle_1_deg 6.085 r_scangle_it 3.006 r_scbond_it 1.804 r_angle_refined_deg 1.333 r_mcangle_it 0.922 r_mcbond_it 0.457 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 23964 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms
Software Software Software Name Purpose BSS data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling