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Crystal structure of the rat cytosolic PCK1, acetylated on Lys244
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QF2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 PEG 3350
magnesium formate
HEPES pH 8
NaF
Crystal Properties Matthews coefficient Solvent content 2.21 44.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.384 α = 90 b = 85.225 β = 90 c = 119.669 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 PILATUS3 S 6M 2018-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97 ALBA XALOC
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 1.75 20 87.3 0.091 0.997 13.2 5.7 55039
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.84 0.874
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 2QF2 1.75 19.95 52817 2167 87.21 0.17201 0.17037 0.1836 0.21151 0.2204 RANDOM 23.795
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] -1.01 1.87 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.529 r_dihedral_angle_4_deg 18.868 r_dihedral_angle_3_deg 15.545 r_long_range_B_refined 8.737 r_long_range_B_other 8.731 r_dihedral_angle_1_deg 7.332 r_scangle_other 4.33 r_mcangle_it 2.855 r_mcangle_other 2.855 r_scbond_it 2.802
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.529 r_dihedral_angle_4_deg 18.868 r_dihedral_angle_3_deg 15.545 r_long_range_B_refined 8.737 r_long_range_B_other 8.731 r_dihedral_angle_1_deg 7.332 r_scangle_other 4.33 r_mcangle_it 2.855 r_mcangle_other 2.855 r_scbond_it 2.802 r_scbond_other 2.802 r_mcbond_it 1.896 r_mcbond_other 1.896 r_angle_refined_deg 1.575 r_angle_other_deg 0.548 r_chiral_restr 0.072 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4872 Nucleic Acid Atoms Solvent Atoms 435 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing