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Crystal structure of effector binding domain of central glycolytic gene regulator (CggR) from Bacillus subtilis in complex with effector fructose-1,6-bisphosphate
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 Ammonium formate pH 6.6, 20% (w/v) PEG 3350. 25mg/ml protein with 90mM fructose-1,6-bisphosphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.26 45.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.447 α = 90 b = 83.245 β = 90 c = 116.457 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 2007-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97900 APS 19-ID
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 1.7 23.94 91.4 0.073 21.86 4.7 50944 -3 29
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 1.7 1.76 94.2 0.66 2 4.2
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 2OKG 1.7 22.64 50942 2727 96.33 0.2035 0.20067 0.2032 0.25678 0.2583 RANDOM 31.484
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] 0.46 -0.54 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.652 r_dihedral_angle_3_deg 12.945 r_dihedral_angle_4_deg 10.268 r_dihedral_angle_1_deg 5.491 r_scangle_it 2.599 r_scbond_it 1.738 r_angle_refined_deg 1.398 r_mcangle_it 0.9 r_mcbond_it 0.618 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.652 r_dihedral_angle_3_deg 12.945 r_dihedral_angle_4_deg 10.268 r_dihedral_angle_1_deg 5.491 r_scangle_it 2.599 r_scbond_it 1.738 r_angle_refined_deg 1.398 r_mcangle_it 0.9 r_mcbond_it 0.618 r_nbtor_refined 0.3 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.207 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.151 r_chiral_restr 0.094 r_bond_refined_d 0.014 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 3765 Nucleic Acid Atoms Solvent Atoms 635 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing