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Crystal structure of the GAF domain from Acinetobacter phosphoenolpyruvate-protein phosphotransferase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 0.1M Tris-HCl pH 8.5, 0.2M MgCl2, 30% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.73 28.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.081 α = 90 b = 54.992 β = 90 c = 124.118 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 2008-02-02 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97931, 0.97945 APS 19-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 1.55 50 99.2 0.095 9 10.3 39536 39536 -3 17.2
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 1.55 1.59 100 0.501 3.9 9.9 2589
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.55 41.17 39430 39430 1983 99.24 0.17 0.17 0.168 0.1967 0.196 0.2182 RANDOM 11.117
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] -0.43 1.14 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.111 r_dihedral_angle_4_deg 20.745 r_dihedral_angle_3_deg 14.83 r_dihedral_angle_1_deg 5.916 r_scangle_it 4.03 r_scbond_it 3.003 r_angle_refined_deg 1.538 r_mcangle_it 1.495 r_mcbond_it 1.311 r_angle_other_deg 0.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.111 r_dihedral_angle_4_deg 20.745 r_dihedral_angle_3_deg 14.83 r_dihedral_angle_1_deg 5.916 r_scangle_it 4.03 r_scbond_it 3.003 r_angle_refined_deg 1.538 r_mcangle_it 1.495 r_mcbond_it 1.311 r_angle_other_deg 0.924 r_mcbond_other 0.256 r_symmetry_vdw_other 0.251 r_nbd_refined 0.241 r_symmetry_hbond_refined 0.191 r_nbd_other 0.189 r_symmetry_vdw_refined 0.178 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.094 r_nbtor_other 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2515 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 48
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MLPHARE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building