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Crystal structure of cyclic nucleotide-binding domain containing protein from Listeria monocytogenes EGD-e
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 1.0 M tri-Sodium Citrate, 0.1 M Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.29 62.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.987 α = 90 b = 91.987 β = 90 c = 144.079 γ = 120
Symmetry Space Group P 65 2 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 MARMOSAIC 225 mm CCD beryllium lenses 2014-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.21 50 99.8 0.095 34.9 21.3 18733 18733 -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 2.21 2.25 100 0.68 4.9 21.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2.21 50 17762 17762 920 99.71 0.20792 0.20607 0.2135 0.24253 0.2436 RANDOM 67.671
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] 0.73 0.36 0.73 -2.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.389 r_dihedral_angle_4_deg 22.645 r_dihedral_angle_3_deg 16.973 r_long_range_B_refined 8.98 r_long_range_B_other 8.971 r_dihedral_angle_1_deg 6.733 r_scangle_other 6.041 r_mcangle_it 4.704 r_mcangle_other 4.702 r_scbond_it 3.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.389 r_dihedral_angle_4_deg 22.645 r_dihedral_angle_3_deg 16.973 r_long_range_B_refined 8.98 r_long_range_B_other 8.971 r_dihedral_angle_1_deg 6.733 r_scangle_other 6.041 r_mcangle_it 4.704 r_mcangle_other 4.702 r_scbond_it 3.968 r_scbond_other 3.968 r_mcbond_other 3.221 r_mcbond_it 3.22 r_angle_refined_deg 1.722 r_angle_other_deg 0.832 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 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 1736 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection HKL-3000 phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling