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Subatomic resolution structure of a high affinity periplasmic phosphate-binding protein (PfluDING) bound with phosphate at pH 4.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G62 PDB ENTRY 3G62
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 4% PEG 8000, 100 mM acetate buffer pH 4.5, 200 mM Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.16 42.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.96 α = 90 b = 124.37 β = 116.55 c = 41.01 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 CCD ADSC QUANTUM 315 2006-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.953 ESRF ID29
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 0.98 36.69 98.1 185558 2 2
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 3G62 0.98 36.69 176838 9308 98.65 0.08814 0.08773 0.0869 0.09591 0.0946 RANDOM 8.948
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] -0.25 -0.1 0.06 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.791 r_dihedral_angle_4_deg 16.669 r_sphericity_free 16.447 r_dihedral_angle_3_deg 12.193 r_rigid_bond_restr 10.138 r_sphericity_bonded 7.516 r_dihedral_angle_1_deg 6.538 r_angle_refined_deg 2.216 r_angle_other_deg 1.074 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.791 r_dihedral_angle_4_deg 16.669 r_sphericity_free 16.447 r_dihedral_angle_3_deg 12.193 r_rigid_bond_restr 10.138 r_sphericity_bonded 7.516 r_dihedral_angle_1_deg 6.538 r_angle_refined_deg 2.216 r_angle_other_deg 1.074 r_chiral_restr 0.11 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_bond_other_d 0.008 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2698 Nucleic Acid Atoms Solvent Atoms 1234 Heterogen Atoms 26
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling