☰ Navigation Tabs
Crystal structure of nucleoside diphosphate kinase from Giardia lamblia featuring a disordered dinucleotide binding site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NPK PDB ENTRY 1NPK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.9 289 GilaA.00438.a.A1 PW27083 at 24.97 mg/mL in 25 mM Hepes pH 7.0, 0.5 M NaCl, 5% glycerol, 2 mM DTT, 0.025% azide against CSHT C11 focus screen 0.1 M Hepes pH 7.0, 0.9 M Na phosphate, 0.9 M K phosphate with 25% ethylene glycol as cryo-protectant, crystal tracking ID 216300h9, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.62 65.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.96 α = 90 b = 116.96 β = 90 c = 62.69 γ = 120
Symmetry Space Group P 63 2 2
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 ADSC QUANTUM 315r 2011-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97946 ALS 5.0.1
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 2.65 50 98.8 0.049 26.02 5.6 7760 7665 -3 60.858
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) 2.65 2.72 100 0.526 3.26 6 567
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 1NPK 2.65 39.4 7619 348 98.26 0.2359 0.2344 0.2392 0.2663 0.2604 RANDOM 78.7938
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] 1.33 0.67 1.33 -2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.361 r_dihedral_angle_4_deg 28.396 r_dihedral_angle_3_deg 14.313 r_dihedral_angle_1_deg 6.811 r_scangle_it 2.695 r_mcangle_it 1.571 r_scbond_it 1.539 r_angle_refined_deg 1.278 r_mcbond_it 0.854 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.361 r_dihedral_angle_4_deg 28.396 r_dihedral_angle_3_deg 14.313 r_dihedral_angle_1_deg 6.811 r_scangle_it 2.695 r_mcangle_it 1.571 r_scbond_it 1.539 r_angle_refined_deg 1.278 r_mcbond_it 0.854 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 813 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 1
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction BOS data collection XDS data reduction