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Crystal structure of effector binding domain of central glycolytic gene regulator (CggR) from Bacillus subtilis in complex with fructose-6-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OKG PDB entry 2OKG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 298 Reservoir: 0.2M Thiocyanate pH 6.6, 20% (w/v) PEG 3350. 25mg/ml protein with 10mM fructose-6-phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.39 48.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.462 α = 90 b = 83.683 β = 90 c = 113.747 γ = 90
Symmetry Space Group P 21 21 21
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 MAR CCD 165 mm 2007-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97900 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 49.85 97.2 0.1 21.82 6.3 45227 -3 20.2
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 1.85 1.92 97.2 3 5.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2OKG 1.85 49.85 42926 2284 98.7 0.1633 0.1609 0.20965 0.2113 RANDOM 20.097
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] 0.98 -0.74 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.94 r_dihedral_angle_3_deg 13.293 r_dihedral_angle_4_deg 12.332 r_dihedral_angle_1_deg 5.042 r_scangle_it 3.379 r_scbond_it 1.983 r_angle_refined_deg 1.446 r_mcangle_it 1.062 r_mcbond_it 0.593 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.94 r_dihedral_angle_3_deg 13.293 r_dihedral_angle_4_deg 12.332 r_dihedral_angle_1_deg 5.042 r_scangle_it 3.379 r_scbond_it 1.983 r_angle_refined_deg 1.446 r_mcangle_it 1.062 r_mcbond_it 0.593 r_nbtor_refined 0.299 r_nbd_refined 0.231 r_symmetry_vdw_refined 0.203 r_xyhbond_nbd_refined 0.194 r_symmetry_hbond_refined 0.171 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3782 Nucleic Acid Atoms Solvent Atoms 622 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing