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2.7 Angstrom Crystal Structure of ABC transporter ATPase from Vibrio vulnificus in Complex with Adenylyl-imidodiphosphate (AMP-PNP)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 295 Protein: 5.9 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3), 1mM AMPPNP;
Screen: PACT (C2), 0.1M PCB buffer (pH 5.0), 25% (w/v) PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.17 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.957 α = 90 b = 104.957 β = 90 c = 85.354 γ = 120
Symmetry Space Group P 31 2 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 MARMOSAIC 225 mm CCD 2014-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.7 30 100 0.117 0.117 32.5 11 15243 15243 -3 57.9
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 2.7 2.75 100 0.621 5 11.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.7 28.55 13687 1535 99.8 0.19991 0.1941 0.25555 0.2376 RANDOM 55.709
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 -0.08 -0.15 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.501 r_dihedral_angle_4_deg 7.935 r_dihedral_angle_3_deg 7.764 r_long_range_B_refined 4.125 r_long_range_B_other 4.086 r_mcangle_it 2.049 r_mcangle_other 2.049 r_scangle_other 1.928 r_dihedral_angle_1_deg 1.771 r_mcbond_it 1.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.501 r_dihedral_angle_4_deg 7.935 r_dihedral_angle_3_deg 7.764 r_long_range_B_refined 4.125 r_long_range_B_other 4.086 r_mcangle_it 2.049 r_mcangle_other 2.049 r_scangle_other 1.928 r_dihedral_angle_1_deg 1.771 r_mcbond_it 1.156 r_mcbond_other 1.155 r_scbond_it 1.147 r_scbond_other 1.147 r_angle_refined_deg 1.051 r_angle_other_deg 0.67 r_chiral_restr 0.062 r_gen_planes_refined 0.019 r_gen_planes_other 0.015 r_bond_refined_d 0.004 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4297 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement BLU-MAX data collection HKL-3000 phasing HKL-3000 data scaling PHENIX phasing