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Crystal structure of pyrophosphate-dependent phosphoenolpyruvate carboxykinase (PPi-PEPCK)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 HEPES, PEG 400, magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.93 57.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.439 α = 90 b = 160.439 β = 90 c = 200.16 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS PILATUS3 6M 2016-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.97887 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.6 48.12 100 0.049 0.999 19.2 20.1 91847
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 0.389 0.837
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.6 48.12 87201 4595 99.97 0.19803 0.19576 0.1951 0.2414 0.2335 RANDOM 54.565
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] -24.11 -24.11 48.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.501 r_dihedral_angle_4_deg 17.773 r_dihedral_angle_3_deg 17 r_long_range_B_refined 9.974 r_long_range_B_other 9.971 r_scangle_other 7.384 r_dihedral_angle_1_deg 7.014 r_mcangle_other 6.813 r_mcangle_it 6.812 r_scbond_it 4.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.501 r_dihedral_angle_4_deg 17.773 r_dihedral_angle_3_deg 17 r_long_range_B_refined 9.974 r_long_range_B_other 9.971 r_scangle_other 7.384 r_dihedral_angle_1_deg 7.014 r_mcangle_other 6.813 r_mcangle_it 6.812 r_scbond_it 4.863 r_scbond_other 4.863 r_mcbond_it 4.615 r_mcbond_other 4.612 r_angle_refined_deg 1.756 r_angle_other_deg 1.323 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 17120 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling AutoSol phasing