☰ Navigation Tabs
Structure of Escherichia coli HrpA in complex with ADP and dinucleotide dCdC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.03M NaNO3
0.03M Na2HPO4
0.03L (NH4)2SO4
0.1M MES-Imidazole
20% ethylene glycol
10% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.2 44.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.47 α = 90 b = 106.124 β = 90 c = 178.276 γ = 90
Symmetry Space Group P 21 21 21
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 DECTRIS PILATUS 6M 2019-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979183 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.257 91.19 96.6 0.219 0.228 0.063 0.993 15.5 13 70047 28.45
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.257 2.295 99.8 1.71 1.776 0.476 0.807 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.26 89.14 1.36 70041 3466 96.56 0.1918 0.1897 0.1875 0.2315 0.23 46.71
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.1866 f_angle_d 1.1861 f_chiral_restr 0.0628 f_bond_d 0.0085 f_plane_restr 0.0073
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9383 Nucleic Acid Atoms 39 Solvent Atoms 583 Heterogen Atoms 61
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing