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Crystal structure of GlxR transcription factor from Corynebacterium glutamicum with cAMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I54 PDB entry 3I54
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293.15 0.1 M Morpheus buffer 3 (Tris; Bicine), 30% Morpheus GOL_P4K (Glycerol, PEG4K), Morpheus Alcohols Mix at 0.12 M, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.05 39.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.248 α = 90 b = 111.248 β = 90 c = 186.951 γ = 120
Symmetry Space Group P 31 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 100 CCD MARMOSAIC 225 mm CCD 2010-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.979 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.38 67.09 99.1 5.7 53828
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.38 2.53 94.8 2.55 5.1 15910
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 PDB entry 3I54 2.38 67.09 51087 2742 99.37 0.21415 0.21015 0.2061 0.28786 0.2787 RANDOM 42.563
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.715 r_dihedral_angle_3_deg 19.128 r_dihedral_angle_4_deg 18.521 r_dihedral_angle_1_deg 6.619 r_scangle_it 3.921 r_scbond_it 2.412 r_angle_refined_deg 1.719 r_mcangle_it 1.515 r_mcbond_it 0.812 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.715 r_dihedral_angle_3_deg 19.128 r_dihedral_angle_4_deg 18.521 r_dihedral_angle_1_deg 6.619 r_scangle_it 3.921 r_scbond_it 2.412 r_angle_refined_deg 1.719 r_mcangle_it 1.515 r_mcbond_it 0.812 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10387 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 156
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction