☰ Navigation Tabs
High-resolution structure of the DING protein from Pseudomonas fluorescens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CAP Human Phosphate-binding protein (HPBP) PDB code 2cap
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 24% PEG 8000, 100 mM acetate buffer pH 4.5, 200 mM Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.12 42.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.728 α = 90 b = 123.679 β = 116.71 c = 40.833 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 MARMOSAIC 225 mm CCD 2006-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9535 ESRF BM14
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 1.43 61.9 98.1 0.026 38.9 4 60045 59063 8.9
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 1.43 1.5 89.2 0.102 10.52 2.9 7166
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 Human Phosphate-binding protein (HPBP) PDB code 2cap 1.43 61.9 59063 2954 100 0.133 0.131 0.1299 0.164 0.1634 RANDOM 10.155
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] -0.28 -0.19 -0.26 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.416 r_dihedral_angle_4_deg 12.15 r_dihedral_angle_3_deg 11.269 r_dihedral_angle_1_deg 5.714 r_sphericity_free 2.155 r_scangle_it 1.687 r_sphericity_bonded 1.51 r_scbond_it 1.206 r_angle_refined_deg 1.119 r_mcangle_it 0.869
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.416 r_dihedral_angle_4_deg 12.15 r_dihedral_angle_3_deg 11.269 r_dihedral_angle_1_deg 5.714 r_sphericity_free 2.155 r_scangle_it 1.687 r_sphericity_bonded 1.51 r_scbond_it 1.206 r_angle_refined_deg 1.119 r_mcangle_it 0.869 r_rigid_bond_restr 0.617 r_mcbond_it 0.553 r_nbtor_refined 0.304 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.15 r_symmetry_hbond_refined 0.12 r_xyhbond_nbd_refined 0.095 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2698 Nucleic Acid Atoms Solvent Atoms 766 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MxCuBE data collection XDS data reduction XSCALE data scaling MOLREP phasing