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Crystal structure of LacI family transcriptional regulator CCPA from Weissella paramesenteroides, Target EFI-512926, with bound glucose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 protein in 10 mM Bis-Tris, 500 mM sodium chloride, 10% glycerol, 5 mM DTT, TEV protease (1:100 ratio), reservoir: 0.641 M malonic acid, 0.088 M ammonium citrate tribasic, 0.042 M succinic acid, 0.105 M DL-malic acid, 0.14 M sodium acetate, 0.175 M sodium formate, 0.056 M ammonium tartrate dibasic, cryoprotectant = reservoir + 100 mM glucose, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.59 52.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.564 α = 90 b = 102.564 β = 90 c = 128.055 γ = 90
Symmetry Space Group P 43 21 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 CCD ADSC QUANTUM 315r mirrors 2014-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.76 50 98.3 0.077 0.077 33.3 12 67129 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.79 100 0.61 0.61 4.6 11.7
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 1.76 50 64875 2066 98.16 0.16854 0.16757 0.1816 0.19826 0.2092 RANDOM 35.069
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] -0.11 -0.11 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.062 r_long_range_B_other 16.338 r_long_range_B_refined 16.166 r_scangle_other 16.112 r_scbond_it 15.891 r_scbond_other 15.891 r_dihedral_angle_3_deg 12.861 r_dihedral_angle_4_deg 12.633 r_mcangle_other 8.271 r_mcangle_it 8.242
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.062 r_long_range_B_other 16.338 r_long_range_B_refined 16.166 r_scangle_other 16.112 r_scbond_it 15.891 r_scbond_other 15.891 r_dihedral_angle_3_deg 12.861 r_dihedral_angle_4_deg 12.633 r_mcangle_other 8.271 r_mcangle_it 8.242 r_mcbond_it 7.562 r_mcbond_other 7.492 r_dihedral_angle_1_deg 5.894 r_angle_refined_deg 1.344 r_angle_other_deg 0.886 r_chiral_restr 0.099 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 4228 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms 24
Software Software Software Name Purpose CBASS data collection SHELX model building ARP/wARP model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SHELX phasing