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C4-type pyruvate phosphate dikinase: conformational intermediate of 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 6.5 285.15 0.1 M MES (pH 6.5), 0.3 M MgCl2, 10% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.8 55.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.159 α = 90 b = 126.515 β = 90 c = 218.998 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 PIXEL DECTRIS PILATUS 6M-F KB mirrors 2016-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9686 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.9 219 99.8 0.047 0.999 20.1 4.9 46486
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 99.7 0.499 0.871 5.2
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 2.9 109.79 46418 2229 99.61 0.2492 0.2474 0.2443 0.2864 0.2782 RANDOM 99.0676
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] 4.41 -0.64 -3.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.413 r_dihedral_angle_4_deg 13.251 r_dihedral_angle_3_deg 11.319 r_dihedral_angle_1_deg 5.616 r_angle_other_deg 3.933 r_angle_refined_deg 1.528 r_mcangle_it 0.553 r_mcbond_it 0.307 r_mcbond_other 0.307 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.413 r_dihedral_angle_4_deg 13.251 r_dihedral_angle_3_deg 11.319 r_dihedral_angle_1_deg 5.616 r_angle_other_deg 3.933 r_angle_refined_deg 1.528 r_mcangle_it 0.553 r_mcbond_it 0.307 r_mcbond_other 0.307 r_chiral_restr 0.082 r_bond_refined_d 0.017 r_gen_planes_other 0.012 r_gen_planes_refined 0.006 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11954 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 64
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing BUCCANEER model building REFMAC refinement PHENIX refinement PDB_EXTRACT data extraction