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C3-type pyruvate phosphate dikinase: intermediate state of the central domain in the swiveling mechanism
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JVL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 285.15 17 % (w/v) PEG 4000, 15 % (w/v) glycerol, 85 mM HEPES (pH 7.5), 5 % (v/v) isopropanol, 10 mM phosphoenol pyruvate, 2.5 mM magnesium sulfate, 1 mM 2'-Br-dAppNHp
Crystal Properties Matthews coefficient Solvent content 4 68.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 249.43 α = 90 b = 249.43 β = 90 c = 84.06 γ = 120
Symmetry Space Group P 6 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 PIXEL DECTRIS PILATUS3 6M Toroidal mirror 2015-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976252 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.9 49.54 99.9 0.089 0.999 13.9 6.9 34537 65.68
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 2.9 3.04 100 0.597 2.7 6.8
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 5JVL 2.9 49.54 34536 1695 99.87 0.1996 0.1978 0.2045 0.2352 0.2406 RANDOM 90.5836
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] 1.68 0.84 1.68 -5.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.861 r_dihedral_angle_4_deg 15.835 r_dihedral_angle_3_deg 14.07 r_dihedral_angle_1_deg 4.788 r_angle_other_deg 3.682 r_mcangle_it 3.084 r_mcbond_it 1.933 r_mcbond_other 1.93 r_angle_refined_deg 1.149 r_chiral_restr 0.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.861 r_dihedral_angle_4_deg 15.835 r_dihedral_angle_3_deg 14.07 r_dihedral_angle_1_deg 4.788 r_angle_other_deg 3.682 r_mcangle_it 3.084 r_mcbond_it 1.933 r_mcbond_other 1.93 r_angle_refined_deg 1.149 r_chiral_restr 0.054 r_bond_refined_d 0.01 r_gen_planes_other 0.005 r_gen_planes_refined 0.004 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6496 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 42
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing BUCCANEER model building REFMAC refinement PDB_EXTRACT data extraction