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Crystal structure of the G alpha protein AtGPA1 from Arabidopsis thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FQJ PDB ENTRY 1FQJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 CRYSTALS OF ATGPA1 WERE GROWN AT 4 DEGREES CELSIUS USING THE HANGING-DROP VAPOR-DIFFUSION METHOD. DROPS CONTAINED 1.5 UL OF PROTEIN SOLUTION (20 MG/ML ATGPA1 IN 25 MM TRIS-HCL, PH 7.4, 5% (V/V) GLYCEROL, 150 MM SODIUM CHLORIDE, 1 MM DTT, 500 UL GTP-GAMMA-S) AND WERE EQUILIBRATED AGAINST 1.5 UL OF 0.3 M MAGNESIUM SULFATE, 0.1 M SODIUM CACODYLATE, PH 6.0, 21% (W/V) PEG 8000. INITIALLY OBTAINED CRYSTALS WERE USED FOR MACROSEEDING. CRYSTALS REACHED THEIR FINAL ROD-SHAPE FORM WITHIN 14 DAYS AFTER MACROSEEDING AND WERE CRYOPROTECTED IN THE MOTHER LIQUOR WITH 8% (V/V) GLYCEROL.
Crystal Properties Matthews coefficient Solvent content 2.6 53.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.13 α = 90 b = 119.347 β = 90 c = 161.725 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 MARRESEARCH MX300 CUSTOM 2009-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
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 2.34 44.6 100 0.11 17.5 6 55808 -3 52.9
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 2.34 2.36 100 0.84 1.9 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 PDB ENTRY 1FQJ 2.34 96.03 54216 1520 99.89 0.21247 0.2113 0.2044 0.25378 0.2473 RANDOM 44.512
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] 0.03 1.37 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.609 r_dihedral_angle_4_deg 19.857 r_dihedral_angle_3_deg 15.294 r_dihedral_angle_1_deg 5.256 r_scangle_it 2.368 r_scbond_it 1.473 r_angle_refined_deg 1.249 r_mcangle_it 0.802 r_mcbond_it 0.407 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.609 r_dihedral_angle_4_deg 19.857 r_dihedral_angle_3_deg 15.294 r_dihedral_angle_1_deg 5.256 r_scangle_it 2.368 r_scbond_it 1.473 r_angle_refined_deg 1.249 r_mcangle_it 0.802 r_mcbond_it 0.407 r_nbtor_refined 0.304 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.188 r_symmetry_hbond_refined 0.157 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.079 r_metal_ion_refined 0.043 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_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7505 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing