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Binding of nucleotides to NDP kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KDN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 METHOD: HANGING DROP IN DROP: 5MG/ML PROTEIN, 50 MM TRIS HCL PH8.5, 8.5MM 3'-AMINO-ADP,15-16% PEG550, 20MM MGCL2 IN WELL: 30-32% PEG550, 50MM TRISHCL PH8.5., pH 8.50
Crystal Properties Matthews coefficient Solvent content 2.26 31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.62 α = 90 b = 71.62 β = 90 c = 153.8 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277 IMAGE PLATE M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LURE BEAMLINE DW32 0.97 LURE DW32
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 15 99.7 0.049 4 23760 2 27
Refinement Statistics Diffraction ID Structure Solution Method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1KDN 2.6 15 2 13728 94.3 0.22 0.22 0.212 0.325 0.3035 RANDOM 30.3
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 x_angle_deg 1.9 x_improper_angle_d 1.68 x_bond_d 0.014 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot
RMS Deviations Key Refinement Restraint Deviation x_angle_deg 1.9 x_improper_angle_d 1.68 x_bond_d 0.014 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot x_mcbond_it x_mcangle_it x_scbond_it x_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3441 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 81
Software Software Software Name Purpose X-PLOR refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing