☰ Navigation Tabs
Transition state mimic of nucleoside-diphosphate kinase from borrelia burgdorferi with bound vanadate and adp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DI6 pdb entry 4DI6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 EBS INTERNAL TRACKING NUMBER ACTIVATED SODIUM ORTHOVANADATE, 2 MM ADP, BOBUA.00664.A.A1_ PS00257 AT 17 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
Crystal Properties Matthews coefficient Solvent content 2.23 44.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.65 α = 90 b = 81 β = 90 c = 181.43 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 CCD MARCCD 300 2012-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.2 99.47 99.6 0.053 17.32 87269 -3 40.87
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) 1 2.2 2.26 99.47 0.311 3.6
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 4DI6 2.2 99.47 59351 3003 0.185 0.183 0.1812 0.223 0.2205 RANDOM 36.587
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] 0.31 -1.51 1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.38 r_dihedral_angle_3_deg 15.017 r_dihedral_angle_4_deg 13.85 r_dihedral_angle_1_deg 5.808 r_angle_refined_deg 1.406 r_chiral_restr 0.098 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8065 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 116
Software Software Software Name Purpose PHASER phasing REFMAC refinement