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The crystal structure of a thermophilic TRAP periplasmic binding protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 290 0.1M Phosphate/Citrate pH4.2, 2.5M Ammonium Sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.91 57.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.26 α = 90 b = 119.26 β = 90 c = 429.1 γ = 120
Symmetry Space Group P 65 2 2
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 300 mm CCD 2005-03-14 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97167, 0.97934, 0.97920 APS 22-ID
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 1.9 103.282 100 0.094 0.094 6.2 9.6 142555 142555
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 2 100 0.405 0.405 1.9 8.4 20471
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 1.9 30 142411 142411 7152 100 0.215 0.215 0.213 0.2183 0.239 0.243 RANDOM 23.493
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] 1.1 0.55 1.1 -1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.398 r_dihedral_angle_4_deg 17.595 r_dihedral_angle_3_deg 14.701 r_dihedral_angle_1_deg 5.844 r_scangle_it 2.561 r_scbond_it 1.751 r_angle_refined_deg 1.249 r_mcangle_it 1.017 r_mcbond_it 0.875 r_angle_other_deg 0.872
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.398 r_dihedral_angle_4_deg 17.595 r_dihedral_angle_3_deg 14.701 r_dihedral_angle_1_deg 5.844 r_scangle_it 2.561 r_scbond_it 1.751 r_angle_refined_deg 1.249 r_mcangle_it 1.017 r_mcbond_it 0.875 r_angle_other_deg 0.872 r_symmetry_vdw_refined 0.263 r_symmetry_vdw_other 0.241 r_nbd_refined 0.21 r_nbd_other 0.183 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.162 r_symmetry_hbond_refined 0.154 r_mcbond_other 0.13 r_nbtor_other 0.085 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10353 Nucleic Acid Atoms Solvent Atoms 529 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction CCP4 data scaling SHELXS phasing