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Subatomic resolution structure of a high affinity periplasmic phosphate-binding protein (PfluDING) bound with arsenate at pH 8.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G63 PDB ENTRY 3G63
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 20-26% PEG 8000, 200mM Li2SO4, 1mM CaCl2, 100mM arsenate pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.14 42.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.9 α = 90 b = 124.16 β = 116.51 c = 40.9 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 PIXEL PSI PILATUS 6M 2011-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.826 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 0.96 33.02 91.7 0.033 18.89 3.29 188778 183115 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.96 1.05 87.5 0.255 4.06 2.95
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3G63 0.96 33.02 183115 173958 9156 91.72 0.09545 0.09468 0.11004 0.1055 RANDOM 9.834
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] -0.08 -0.04 0.09 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.971 r_sphericity_free 34.41 r_dihedral_angle_4_deg 19.317 r_dihedral_angle_3_deg 11.361 r_sphericity_bonded 7.751 r_rigid_bond_restr 6.926 r_dihedral_angle_1_deg 6.813 r_angle_refined_deg 2.159 r_angle_other_deg 1.274 r_chiral_restr 0.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.971 r_sphericity_free 34.41 r_dihedral_angle_4_deg 19.317 r_dihedral_angle_3_deg 11.361 r_sphericity_bonded 7.751 r_rigid_bond_restr 6.926 r_dihedral_angle_1_deg 6.813 r_angle_refined_deg 2.159 r_angle_other_deg 1.274 r_chiral_restr 0.147 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d 0.011 r_gen_planes_other 0.003 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 991 Heterogen Atoms 5
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling