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Crystal structure of Lactococcus lactis pyruvate carboxylase G746A mutant in complex with cyclic-di-AMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% (w/v) PEG3350, and 0.2 M ammonium formate
Crystal Properties Matthews coefficient Solvent content 2.84 56.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.155 α = 65.99 b = 130.39 β = 88.67 c = 134.271 γ = 70.14
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 2016-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.987 APS 24-ID-C
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 2 50 92.3 0.059 12.5 2.3 349241 -3
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 2.07 90.4 0.492 1.7 2
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 48.55 331624 17612 92.12 0.19223 0.19087 0.2017 0.21814 0.2287 RANDOM 41
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] 1.1 2.61 -1.45 0.22 -0.27 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.979 r_dihedral_angle_4_deg 20.486 r_dihedral_angle_3_deg 16.284 r_dihedral_angle_1_deg 6.18 r_angle_refined_deg 1.608 r_angle_other_deg 1.088 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_gen_planes_other 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.979 r_dihedral_angle_4_deg 20.486 r_dihedral_angle_3_deg 16.284 r_dihedral_angle_1_deg 6.18 r_angle_refined_deg 1.608 r_angle_other_deg 1.088 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_gen_planes_other 0.007 r_bond_other_d 0.006 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 35206 Nucleic Acid Atoms Solvent Atoms 1217 Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing