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Crystal structure of AMP-PNP bound Enterococcus hirae V1-ATPase [bV1]
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 20% PEG 3350, 0.1M Bis-Tris propane, 0.2M sodium fluoride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.31 46.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.149 α = 90 b = 127.416 β = 90 c = 225.252 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 270 2011-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.0000 Photon Factory BL-1A
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 2.68 50 96.1 0.154 9.57 5.7 97250 97250 57.971
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 2.69 2.79 89.2 0.767 1.76 4.9 8899
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3VR4 2.68 48.58 92330 92330 4864 100 0.18481 0.18481 0.18159 0.24618 0.2334 RANDOM 43.541
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] 0.15 -2.86 2.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.82 r_dihedral_angle_4_deg 21.225 r_dihedral_angle_3_deg 19.52 r_dihedral_angle_1_deg 5.349 r_scangle_it 2.675 r_scbond_it 1.529 r_angle_refined_deg 1.273 r_mcangle_it 0.859 r_mcbond_it 0.429 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.82 r_dihedral_angle_4_deg 21.225 r_dihedral_angle_3_deg 19.52 r_dihedral_angle_1_deg 5.349 r_scangle_it 2.675 r_scbond_it 1.529 r_angle_refined_deg 1.273 r_mcangle_it 0.859 r_mcbond_it 0.429 r_chiral_restr 0.087 r_bond_refined_d 0.011 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 26497 Nucleic Acid Atoms Solvent Atoms 500 Heterogen Atoms 64
Software Software Software Name Purpose SERGUI data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling