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Crystal Structure of ApcT K158A Transporter Bound to 7F11 Monoclonal Fab Fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GI9 ApcT - Fab complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5 293 0.1M sodium acetate, 0.1M ammonium dihydrogen phosphate, 40-44% PEG 400, pH 5.0, Microbatch, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.07 59.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.039 α = 90 b = 111.188 β = 90.92 c = 115.674 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315 2008-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0332 ALS 5.0.2
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 2.59 50 99.6 0.087 17.4 4.4 36142 -3
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) 2.59 2.69 96.8 0.335 3 3.9
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 ApcT - Fab complex 2.59 50 34311 1803 99.61 0.25629 0.25362 0.2516 0.30685 0.3065 RANDOM 56.772
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] -3.01 2.08 0.11 2.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.595 r_dihedral_angle_3_deg 15.569 r_dihedral_angle_4_deg 14.802 r_dihedral_angle_1_deg 5.222 r_angle_refined_deg 0.935 r_scangle_it 0.773 r_mcangle_it 0.609 r_scbond_it 0.466 r_mcbond_it 0.336 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.595 r_dihedral_angle_3_deg 15.569 r_dihedral_angle_4_deg 14.802 r_dihedral_angle_1_deg 5.222 r_angle_refined_deg 0.935 r_scangle_it 0.773 r_mcangle_it 0.609 r_scbond_it 0.466 r_mcbond_it 0.336 r_nbtor_refined 0.299 r_symmetry_hbond_refined 0.187 r_nbd_refined 0.173 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.11 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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_refined 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6720 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling