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Pyruvate phosphate dikinase in complex with AMP-PNP and sulfate ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KBL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 303 PPDK 25mg/ml with 5mM MgCl2 + 5 mM AMPPNP in 2.3 M ammonium sulfate, 0.1 Na Hepes. Protein solution in 20 mM imidazole buffer, pH 6.5, 100 mM KCl, 0.1 mM EDTA and 1 mM mercaptoethanol
Crystal Properties Matthews coefficient Solvent content 2.84 56.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.695 α = 90 b = 118.475 β = 90.4 c = 170.806 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 IMAGE PLATE RIGAKU RAXIS IV++ 2006-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 3 48 99.4 0.05 12.9 2.3 86567 38
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 3 3.06 96.2 0.208 2.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3 47.533 1.35 86160 4374 99.12 0.2245 0.2187 0.2293 0.3021 0.314 random selection
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] -8.8351 -0.4745 19.2285 -10.3934
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.245 f_angle_d 1.252 f_chiral_restr 0.078 f_bond_d 0.01 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27012 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 184
Software Software Software Name Purpose PHENIX refinement CrystalClear data collection XDS data reduction Aimless data scaling PHASER phasing