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Crystal structures of a sodium-alpha-keto acid binding subunit from a TRAP transporter in its closed forms
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HZK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 293 100mM sodium citrate
1.4M ammonium sulfate
30mM pyruvate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.021 α = 90 b = 78.057 β = 124.98 c = 95.139 γ = 90
Symmetry Space Group C 1 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 2006-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97565 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.4 48 99 137400 137318 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.4 1.41 97.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2HZK 1.4 39.01 137400 137316 6908 100 0.173 0.173 0.173 0.1718 0.184 0.1831 RANDOM 11.164
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] 0.02 -0.06 0.01 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.896 r_dihedral_angle_3_deg 12.769 r_dihedral_angle_4_deg 12.748 r_dihedral_angle_1_deg 5.762 r_scangle_it 2.761 r_scbond_it 1.701 r_angle_refined_deg 1.143 r_mcangle_it 1.038 r_mcbond_it 0.537 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.896 r_dihedral_angle_3_deg 12.769 r_dihedral_angle_4_deg 12.748 r_dihedral_angle_1_deg 5.762 r_scangle_it 2.761 r_scbond_it 1.701 r_angle_refined_deg 1.143 r_mcangle_it 1.038 r_mcbond_it 0.537 r_nbtor_refined 0.312 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.115 r_symmetry_hbond_refined 0.107 r_chiral_restr 0.079 r_metal_ion_refined 0.051 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5304 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling MOLREP phasing